Correct. There are definitely two issues here that need to be handled.

1) I need to be able to program a bootloader and my user program in one step to keep manufacturing costs down.

2) Due to the nature of my bootloader needs, it appears that I have to roll my own.

I think I have a pretty good handle on #1 at this point. I'll be testing that out later today. #2 looks to be much more complicated than I naively assumed it would be. Anyway, time to dig my feet in a little more.