You have to specify each file that will be included in your app. A good place to start would be the step-by-step walkthrough. (Step 6, specifically talks about where you put your files).
Tell me if that helps.
I am considering buying WyBuild for a .NET project I am working on, and I'm trying to figure out how the system knows which files to update when it creates its patches when I seek to update a project in Visual Studio. Or do I have to specify each actual file to update?
You have to specify each file that will be included in your app. A good place to start would be the step-by-step walkthrough. (Step 6, specifically talks about where you put your files).
Tell me if that helps.
It helps, but how do I keep track of which files have been adjusted in Visual Studio since my last update? Is there an easy way to do that?
You don't need to keep track of which files changed. wyBuild does that for you. That's why you need to include all files inside their own folders.