Shes kind of wasting her time with just a deck... the sound is not going to improve very much being the stock amp and speakers are still in there. You'll run into a lot of noise problems if you run the new deck through the stock amp... and the speakers are most likely 2 ohms, when they should be 4... deck amps are not made to handle 2 ohm loads, so if the deck amp does not turn off, it will run very hot and be damaged over time.

Her best bet is going to be to bypass the entire Bose system... install a new deck with a wirring harness, bypass the amp (you can buy an adapter, or find the wirring diagram and splice the wires yourself) and run new speakers.

Bose always liked to make it hard to add on to their stock stereos... just another reason they suck so bad.