You're basically saying that I can put a zip file on a web page that they can go to and download into the same directory as the software to be updated.
Yes.
Configure the update on the server side.
Well, you do this before the first one. So, let's say the version these users have installed is version "4.4". In wyBuild you'll have a version "4.4" tab in which all the version 4.4 files are.
Then you build the wyUpdate (by clicking "Build wyUpdate") and make sure the dropdown above that button says "Create wyUpdate for inclusion with version 4.4 of your product." If the version isn't correct, then click the dropdown and select the correct version from the list. Then click Build wyUpdate.
Those wyUpdate.exe and client.wyc files rew what the users will be putting in your application's directory.
Then you can add the next version of your app to wyBuild (let's call it version 4.5). Add the files (as described in step 6 of the walkthrough), then Build the updates and then upload them to your server.
Then they run the wyUpdate.exe file and it will know which files to pull from the wyUpdate server and install them over the existing installation?
Yes, presuming you did what I said.