Mac mini server Mid 2011 Maverick upgrade problem

Help needed I have a mac mini server mid 2011
2x500gb hard drives
Hard Drive one is Macintosh HD
Hard Drive Two is Server HD
I upgraded to mavericks osx onto drive one Macintosh HD
I went to upgrade os x server for mavericks and it went to install on hard drive one Macintosh HD not the Server HD
So I formated both drives which partition map scheme is GUID Partition Table on both drives.
I done a new Install of Mavericks on drive one Macintosh HD that works fine
I downloaded OS X Server again and it is installing on hard drive one Macintosh HD and not Server HD
and it will not give me an option to Install on the Server HD.
I have also looked in the system preferances Startup disk and now I have a question mark showing.
When I open it it only shows Macintosh HD and NOT the Server HD
Can someone please advise
I'm not bad on computers but this has stuped me.
Iif anyone can help please can you explain in easy terms if there is any.
Thank you

Server.app will install on the same disk OS X resides on.
What I think you are seeking here is to have the server data on the other disk, and that is configured via Server.app, once you have Server.app installed. Launch Server.app and select the server name at the top of the left column and then go to the Settings on the right side, and select where you want the service data there.

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