If you wish to sync an iOS device to your server iTunes instance, you should configure it as normal whilst running iTunes interactively through, for example, a remote desktop connection.

 

This Apple article shows how to configure and troubleshoot Wifi connections within iTunes - http://support.apple.com/kb/TS4062

 

If wifi syncing is unreliable despite following these steps, click the 'Restart Apple Mobile Services' check box in iHomeServer settings and then restart iTunes from the iHomeServer Console.  This works around an issue with some versions of iTunes where the Apple Mobile Services is left in an incorrect state after closing iTunes.