The AutomaticUpdater documentation & videos are being created right now - they should be all up by Friday. As far as the UpdateEngine.cs in the wyUpdate source, it has been split into 2 files: ServerFile.cs & ClientFile.cs.
You'll probably want ServerFile.cs as it's more applicable for your application.
Actually, from the way you're using wyUpdate the AutomaticUpdater would be a perfect fit. I'll try to have at least a intro tutorial up by tonight.
Edit (10/6): A few bugs have been found in the AutomaticUpdater control, thus the delayed tutorial. The full documentation should be up by Thursday (definitely by Friday).
At any rate, the methods that you used before will still work (even with the old UpdateEngine.cs).