The Bose system is integrated to work together.
I'm not sure you could use the Bose amp with an aftermarket HU.
Then again, I'm not sure you'd want to.
The Bose system by itself is a good system.
As for upgrading, it's great the speakers and grilles are already installed with the Bose system, and the wires are already ran from the amp in the back to the speaker locations.
Having the Bose system gives you the moonroof, it sounds good, and it will give you easier options when you are ready to upgrade.
Even if you had to lose the Bose amp, you might be able to use a couple of low wattage amps and still use the Bose speakers...... only if you have crossover control with the new HU or the amp/s.
I'm nearly positive the crossover control for specific frequencies to be limited each speaker is controlled via the amp and/or the Bose HU.
For those reading: HU = Head Unit
Sorry, I'm thinking this through as I type.
I will live with the Bose system as long as possible, then do a complete revision when replacing it.
The biggest problem is the normal stereo doesn't have the dash speakers.... or the cutouts in the dash.
Back to one of your questions: The Bose amp is driving 18w to the 3.25" and 35w to the 9" front doors. I'm assuming 18w or less to the rear doors and rear d-pillars.
If your new HU has power, you can use that to drive the rear Bose speakers for low level rear fill. Then use a 4ch amp to drive the front Bose door and dash speakers. (forget the center speaker)
To work with the Bose speakers, you could use a small amp like:
Arc Audio 4050XXK or CXL
Elemental Designs Nine.4
JL Audio 300.4
or an Arc 5150XXK to add a small sub in the back. There's one on eBay currently at $200.
There are many many directions to go with the CX-7 layout.
1) do you want the moonroof?
2) do you need nav, b-tooth, cam, etc?
3) do you want pre-existing dash cutouts or do-it-yourself?
4) overall budget?
hope this rambling of random thoughts help LOL