Has anyone added an amp to a factory Bose unit in a 2000+ SSEi? If so, would you rate is as a DIY project, or strictly for the professional?

Also, what do you consider the best option for aftermarket speakers for the same cars? Why?

yes when an aftermerket stero is added the factory bose is bypassed. although there is an interface that keeps the functoin of the bose amp with an aftermarket headunit.

you will need a power cable, speaker wire, and RCA cables for the new amp.

The deck is basicly stamped with BOSE on the face and/or the chassis of the radio, so the deck is basicly a standard deck.
You will need to rewire from the deck to the amp and then to the speakers. Not an extremely hard job, but you will need a wiring diagram of your stereo system as you will only need to rewire for the speakers, and then just run fused power cable from the battery to the amp and the ground cable.
I'll be doing this fairly soon. Still trying to decide on the proper amp.

as i mentioned there is now a interface that allows you to keep your BOSE amp with an aftermarket deck, but your best bet is just to bypass the BLOSE amp and install an aftermarket one

I am installing 2 amps in my car right now one for the fronts speakers and another for the back, I have a pic write up here soon

its too cold down there to start taking plastic peices off

With the BOSE amp in the trunk (along with all of the speaker wires) and the car'* battery under the back seat, this isn't an extremely hard job. Took me about 1 1/2 hours, including replacing rear speakers with Pioneer 4-ways and running power to the amp.

The difference in sound was worth it.

Yup. It is easy work compared to tranny swaps, and heck easier the doing plugs -practically. Only it takes longer.
I put Infinity 3-ways in the rear of my car running of the otherwise stock system (using a 7-band eq deck instead of the 2-slider deck) and it was incredible. Then I stuck the Alpines in the front doors and I lost alot of mids, highs and even abit of the power to the rears. I am considering putting the BOSE speakers back in the front doors until I get an amp as they sounded better than the non-amped Alpine 2-ways.