In this case you'd be better off using wyUpdate as a standalone updater (since the circumstances are complicated). The AutomaticUpdater was really designed to make updating any one single app easy.
Implementing what you want is a simple matter of letting the user update the server app. Then once the server/client versions mismatch (or however you want to do it) update the client apps.
So, you'll have 2 wyBuild projects. One for your server app. And one for your client apps.
Does that make sense?