I had a question that is I have three domains on a server

I had a question that is I have three domains on a server can I chose what sites I want to make part of the network after I make multisite. Or is it going to pull all of the wordpress sites off my two server's after network insall.
This is were I am confuses I have two servers and I don't want to associate these three sites with that server.
I don't know to much about your multi site will this work.
Please bare with me.

Regards Vinny