03 Tahoe replace Bose

To use a 4 channel amp to power 4 speakers and a factory sub, they probably plan on using the 2 front channels of the amp to run the interior speakers (fronts and rears- 2 speakers per channel), and bridge the rear channels for the sub.  I wouldn't recommend doing this.  However, I can't suggest sticking with the factory sub either.  I'd either use a 5 channel amp with one channel dedicated to run an aftermarket sub/box (you can use a JL stealthbox if you like), or stick with the 4 channel and do away with the sub (at least until you can afford one).  If you want to retain use of the factory sub, I'd only use the factory amp to power it (this may actually be what they're planning to do).

I'd recommend doing away with the 3.5's altogether.  They don't serve much a purpose, and detract from your sound up front (which is where you should want most of it anyway). 

I know this is probably not what you want to be reading right now, but that's my honest opinion.

You can use the factory deck (I'm guessing the Nav is factory) to power the factory sub, it will work fine.  One problem you will run into is retaining the OnStar.  If you aren't replacing the deck, and you try to use a seperate speaker for the OnStar, you will also get music through it. 

If I read this wrong and your Nav is an aftermarket, then just wire up the speaker leads to the OnStar/Bose adaptor, and this will power your factory sub with the Bose Amp.  Although you may still run into the problem with the Onstar, and music coming through the seperate speker.

I wouldn't recommend using the factory sub, and an aftermarket amp.  The factory "sub" is only a 6" speaker.