idabanker, don't take this wrong but HMDA doesn't always make sense. It's a govt regulation, emphasis on govt. LOL just kidding I have been caught too many times trying to make a logical decision, it really doesn't work.
We use App 1 and App 2 for HMDA reporting, GMI, etc. Like AJ said, income is the income you relied on, maybe all 3, or maybe you only considered income of App 1 and App 3. If so, you still show App 1 and 2 on report, but income for App 1 and 3.
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NOLA is my Beach!