Hey Kirk,
From looking through the tutorial and taking the example stated for the server update folder 'http://yoursite.com/updates/%file%', the updater uses the filename for the argument '%file%', am I correct?
Yes, and the filename is formed from the product name, the version "from", and the version "to". This way your updates will never overwrite one-another on your server.
You can always change the default update filename format by going to "File->Properties->Update & server files" in wyBuild:
[attachment=0]update filename.png[/attachment]
In your example (MyApp v1.0 to v1.1) the update filename would be "myapp.1.0.to.1.1.wyu".
Does this make sense?