what is the major difference between the two

Both used paper cones, both used amplifiers, both used dedicated crossovers in the front doors.

Monsoon has more speaker, 8 total. 4 up front (6.25 in the door with tweets), 4 in the back (3.5 in the doors with 6x9s in the rear deck). The 6x9s are wired to be "bass only" from the factory via the stock Monsoon amplifier.

i think your wrong about the amount of speakers and size of the rear door speakers i know that the monsoon and bose both have 8 speakers and the rears are 5.25 in the monsoon not sure about bose but what i really wanted to know is does the bose use the 6x9s as a dedicated sub woofer like the monsoon does

You're right, I got the rear door size wrong. Thanks for correcting me.

On that question I am not sure at all, since my 2002 was a mid-year build that had the Monsoon stuff in it before I gutted it and put my stuff in.