Maybe I am the only one who did not find the option how to prevent Sametime chat windows from popping up for every incoming message in Notes 8.0.1 (resp. Sametime 8.0). I think this option was somewhere else in Notes 8.0 (resp. Sametime 7.5.1).
Anyway, this is how to do it:
Go to "File -> Preferences -> Sametime -> Notifications"
Click on "One-on-one chat"
Uncheck "Bring chat window to front"