Hey Mike,
Step 6 of the walktrhough talks about the first version of your app.
Do I upload the blank / empty update version first and then make a new one for the actual release?
The first version of your app that you're releasing to your users (let's call it 1.0) with wyUpdate.exe will be the first version of your app listed in your wyBuild project. Because no users has any previous version installed, you can build this as a blank update first, then upload the update files. That way when your users with 1.0 check for updates they'll see they have the latest version installed.
Immeditately after you upload the blank update, add your 1.0 files inside wyBuild. Then save your project.
Later, when you release 1.1 of your app, open your wyBuild project again. The new release workflow is to create a new tab (1.1) and add your 1.1 files to it. Now when you build your updates wyBuild will make a small patch from 1.0 of your app to 1.1 of your app.
Does that make sense?