NOT a good idea... and a total waste of time and money. You say it includes the sub... I would assume its from a TL or RSX-S then... which would mean the headunit will NOT fit your car. The TL and RSX-S decks have a large faceplate that integrates into the dash in the respective car... and only those cars.
Bose is rather overly complicated audio, with a huge price tag for no reason. They take very minimal power, at low impedance levels (usually 2 ohms) and power PAPER speakers with decent excursion (the distance the speaker is able to travel)... they use equalization to make it sound decent, but nothing like a good sounding stereo would. The drivers they use are very cheap, at about a dollar or 2 a piece.
The signal from the deck to the amplifier (in acuras a central amp was used... certain other makes of vehicles use amplified speakers [amplifier mounted directly to the speaker]) is also a very LOW level signal with an odd impedance... making integration with a non bose unit VERY difficult. This low level signal takes a lot of shielding to prevent any noise from entering the signal, so you'd need a custom harness to run from the deck to the amp.
You are looking at a total waste of time. If you want improved sound quality use your oem deck with some aftermarket speakers... you'll spend a hell of a lot less money and time installing... and it'll sound 10 times better.
The 98-00 accords used an alpine made deck in the EX models (the single CD, double DIN unit)... 01-02 accords used a pioneer unit (the 6 disc unit).
The cd player in the 97 accord was made by Panasonic, and tends to have some problems over time... not being able to play CDs.
EDIT: I noticed you never said anything about getting the Bose headunit... you can not use the deck in your car with a bose stereo... you'd have a lot of feedback.
Someone mentioned something about the sub being a problem... it wouldnt be, as the amp that came from the car has the ability to power it, it takes the signal from the front and rear signals from the oem deck. (most likely it was a seperate amp for just the sub, which would again complicate the wirring process more).