How to install software that does not show in add\remove?

I have a agent that i need to install on all our computers but the program does not show in add\remove when installed correctly.
It does however have a service that runs and some processes that run.
Can someone tell me what the best way of installing this is?
Should I create a collection based of the Service\Process or even based of the file sitting in C:\Program Files.
I wanted to create a collection of computers that had the software already then create another collection that had all computers with it missing and create a advertisement from this..
I am just not sure how to do this one when it does not show in add\remove

Please create the new SCCM query based collection for computers which have required software installed. We can create this collection based on service. 
For example :Below SCCM query will add the computers which firewall service is in disabled mode.
select SMS_R_SYSTEM.ResourceID,SMS_R_SYSTEM.ResourceType,SMS_R_SYSTEM.Name,SMS_R_SYSTEM.SMSUniqueIdentifier,SMS_R_SYSTEM.ResourceDomainORWorkgroup,SMS_R_SYSTEM.Client from SMS_R_System inner join SMS_G_System_SERVICE on SMS_G_System_SERVICE.ResourceId =
SMS_R_System.ResourceId where SMS_G_System_SERVICE.Name like "MpsSvc" and SMS_G_System_SERVICE.StartMode like "Disabled" 
Create another collection for computers which have software not installed and add the below query for the collection. Replace the "CollectionID" with collectionID of first collection.
select SMS_R_SYSTEM.ResourceID,SMS_R_SYSTEM.ResourceType,SMS_R_SYSTEM.Name,SMS_R_SYSTEM.SMSUniqueIdentifier,SMS_R_SYSTEM.ResourceDomainORWorkgroup,SMS_R_SYSTEM.Client from SMS_R_System where ResourceID not in (select ResourceID from SMS_FullCollectionMembership
where CollectionID = "CollectionID") 

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