How to upgrade the schema on both the sites using sql scripts?

Hi Experts,
I need some help.
I have two sites SITE A and SITEB, on both the sites GG is installed and running (DML Bi- directional replication). I have schema SCHEMA1 on both the sites which are configured for replication and replication is working from last one year.
Now I wanted to upgrade the SCHEMA1 on both the sites. There are three .sql script which has many SQL commands like create table, create sequence, create procedure, insert record etc. I wanted to run that SQL file one both the sites.
So should I stop all the process on both the sites SITEA and SITE B (including manager process) ,execute the SQL scripts on both the sites and then start the process again ? Will it work?
Is there any other best way to do this?
Could you please suggest the steps so that I can successfully execute theses scripts on both the site to upgrade the schema1.

There is no blanket answer here; it depends. Main questions are:
1. Do the SQL scripts update existing tables?
2. Are you replicating DDL in one direction? (DDL should only be replicated one way even when doing bi-directional, do DDL should only be issued on the node capturing DDL
3. Are you using a wildcard (*) from table names or using an explicit list?
Easiest thing is if you're replicating DDL from A to B and apply DDL to A only. This assumes that the application writing to these tables can handle DDL changes under the covers. If these are new tables supporting new application features then you would simply enable said features after apply sql files.
From there it gets more complicated and would need answers to the above questions before going down each line of logic. But try to remember what's really going on here. Data in one form (DDL) is being captured and send along. If the "shape" (DDL) of that data changes then the extract and replicat need to update their meta data to handle it correctly. If change data encounters a different shape than what's cached then you will become out of sync.
I'm not sure if that makes sense but again, the answers to the questions above will be indicate where more detailed explanations should be focused. In short, we need more detail about what those scripts do and your current setup.
Good luck,
-joe

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CM2012 R2 RTM on Server2012 R2 RTM with SQL2012 SP1
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2013-12-01 06:58:24 Detected role services: Api, Database, UI, Services
2013-12-01 06:58:24 Start: LoadSettingsFromXml
2013-12-01 06:58:24 Start: GetConfigValue with filename=UpdateServices-Services.xml item=ContentLocal
2013-12-01 06:58:24 Value is true
2013-12-01 06:58:24 End: GetConfigValue
2013-12-01 06:58:24 Start: GetConfigValue with filename=UpdateServices-Services.xml item=ContentDirectory
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2013-12-01 06:58:24 End: GetConfigValue
2013-12-01 06:58:24 Content directory is D:\sources\wsus
2013-12-01 06:58:24 Start: GetConfigValue with filename=UpdateServices-DB.xml item=InstanceName
2013-12-01 06:58:24 Value is confman
2013-12-01 06:58:24 End: GetConfigValue
2013-12-01 06:58:24 SQL instance name is confman
2013-12-01 06:58:24 End: LoadSettingsFromXml
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2013-12-01 06:58:24 Start: Run
2013-12-01 06:58:24 Fetching WsusAdministratorsSid from registry store
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2013-12-01 06:58:24 Fetching WsusReportersSid from registry store
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2013-12-01 06:58:25 Configuring content directory...
2013-12-01 06:58:25 Configuring groups...
2013-12-01 06:58:26 Starting group configuration for WSUS Administrators...
2013-12-01 06:58:26 Found group in regsitry, attempting to use it...
2013-12-01 06:58:28 Writing group to registry...
2013-12-01 06:58:28 Finished group creation
2013-12-01 06:58:28 Starting group configuration for WSUS Reporters...
2013-12-01 06:58:28 Found group in regsitry, attempting to use it...
2013-12-01 06:58:28 Writing group to registry...
2013-12-01 06:58:28 Finished group creation
2013-12-01 06:58:28 Configuring permissions...
2013-12-01 06:58:28 Fetching content directory...
2013-12-01 06:58:28 Fetching ContentDir from registry store
2013-12-01 06:58:28 Value is D:\sources\wsus
2013-12-01 06:58:28 Fetching group SIDs...
2013-12-01 06:58:28 Fetching WsusAdministratorsSid from registry store
2013-12-01 06:58:28 Value is S-1-5-21-1033354796-2088831985-1429053453-1003
2013-12-01 06:58:28 Fetching WsusReportersSid from registry store
2013-12-01 06:58:28 Value is S-1-5-21-1033354796-2088831985-1429053453-1004
2013-12-01 06:58:28 Creating group principals...
2013-12-01 06:58:28 Granting directory permissions...
2013-12-01 06:58:28 Granting permissions on content directory...
2013-12-01 06:58:29 Granting registry permissions...
2013-12-01 06:58:29 Granting registry permissions...
2013-12-01 06:58:29 Granting registry permissions...
2013-12-01 06:58:29 Configuring shares...
2013-12-01 06:58:29 Configuring network shares...
2013-12-01 06:58:29 Fetching content directory...
2013-12-01 06:58:29 Fetching ContentDir from registry store
2013-12-01 06:58:29 Value is D:\sources\wsus
2013-12-01 06:58:29 Fetching WSUS admin SID...
2013-12-01 06:58:29 Fetching WsusAdministratorsSid from registry store
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2013-12-01 06:58:29 Deleting existing share...
2013-12-01 06:58:29 Creating share...
2013-12-01 06:58:29 Share successfully created
2013-12-01 06:58:29 Creating share "WsusContent" with path "D:\sources\wsus\WsusContent" and description "A network share to be used by Local Publishing to place published content on this WSUS system."
2013-12-01 06:58:29 Deleting existing share...
2013-12-01 06:58:29 Creating share...
2013-12-01 06:58:29 Share successfully created
2013-12-01 06:58:29 Creating share "WSUSTemp" with path "C:\Program Files\Update Services\LogFiles\WSUSTemp" and description "A network share used by Local Publishing from a Remote WSUS Console Instance."
2013-12-01 06:58:29 Deleting existing share...
2013-12-01 06:58:29 Creating share...
2013-12-01 06:58:29 Share successfully created
2013-12-01 06:58:29 Finished creating content shares
2013-12-01 06:58:29 Stopping service WSUSService
2013-12-01 06:58:29 Stopping service W3SVC
2013-12-01 06:58:32 Configuring database...
2013-12-01 06:58:32 Configuring the database...
2013-12-01 06:58:32 Establishing DB connection...
2013-12-01 06:58:32 Checking to see if database exists...
2013-12-01 06:58:32 Database exists
2013-12-01 06:58:32 Switching database to single user mode...
2013-12-01 06:58:32 Loading install type query...
2013-12-01 06:58:32 DECLARE @currentDBVersion       int
DECLARE @scriptMajorVersion     int = (9600)
DECLARE @scriptMinorVersion     int = (16384)
DECLARE @databaseMajorVersion   int
DECLARE @databaseMinorVersion   int
DECLARE @databaseBuildNumber    nvarchar(10)
IF NOT EXISTS(SELECT * FROM sys.databases WHERE name='SUSDB')
BEGIN
    SELECT 1
END
ELSE
BEGIN
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    SET @databaseBuildNumber = (SELECT BuildNumber FROM SUSDB.dbo.tbSchemaVersion WHERE ComponentName = 'CoreDB')
    DECLARE @delimiterPosition INT = CHARINDEX('.', @databaseBuildNumber)
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    BEGIN
        RAISERROR('Invalid schema version number', 16, 1) with nowait
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    SET @databaseMinorVersion = SUBSTRING(@databaseBuildNumber, (@delimiterPosition + 1), (10 - @delimiterPosition))
    IF @currentDBVersion < 926
    BEGIN
        SELECT 3
    END
    ELSE
    BEGIN
        IF (@scriptMajorVersion > @databaseMajorVersion OR
           (@scriptMajorVersion = @databaseMajorVersion AND @scriptMinorVersion > @databaseMinorVersion))
        BEGIN
            SELECT 2
        END
        ELSE IF (@scriptMajorVersion = @databaseMajorVersion AND
                 @scriptMinorVersion = @databaseMinorVersion)
        BEGIN
            SELECT 0
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        ELSE
        BEGIN
            SELECT 4
        END
    END
END
2013-12-01 06:58:33 Install type is: UnsupportedFuture
2013-12-01 06:58:33 DB is a higher version than the config scripts
2013-12-01 06:58:33 Swtching DB to multi-user mode......
2013-12-01 06:58:33 Finished setting multi-user mode
2013-12-01 06:58:33 Microsoft.UpdateServices.Administration.CommandException: The schema version of the database is from a newer version of WSUS
than currently installed. You must either patch your WSUS server to at least
that version or drop the database.
   at Microsoft.UpdateServices.Administration.ConfigureDB.CheckForUnsupportedVersion(DBInstallType installType, Boolean dbExists)
   at Microsoft.UpdateServices.Administration.ConfigureDB.ConnectToDB()
   at Microsoft.UpdateServices.Administration.ConfigureDB.Configure()
   at Microsoft.UpdateServices.Administration.PostInstall.Run()
   at Microsoft.UpdateServices.Administration.PostInstall.Execute(String[] arguments)
Fatal Error: The schema version of the database is from a newer version of WSUS
than currently installed. You must either patch your WSUS server to at least
that version or drop the database.
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Gerry,
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