1. I would just create a single tracking profile for everything.
2. It might be possible to make the ActivityID show up there somehow, but your portal config is limited to what you can do in the activity definition spreadsheet. Unfortunately, the BAM portal is not 100% flexible. The good news is you can use SSRS or write a custom app to view BAM data directly from the database.
3. I think you are going to have to usesomething other than invoice number for the ActivityID when you begin the activity. You can maybe use continuation to allow updating the activity by invoice nuber (http://msdn.microsoft.com/en-us/library/aa559486.aspx). For this one you probably need to use the BAM API instead of a tracking profile. (http://msdn.microsoft.com/en-us/library/aa559502.aspx).