ok this new car has a decent stereo... and i know feck all about ICE so dunno how its supposed to be set up

and it was a bit distorty when the bass was tuned up...
the car's got decent speakers all round, 6x9s i the shelf, 3 sets of tweeters etc. etc. n 2 12inch subs in the boot
its got 2 amps... some big philips one (6040 i think) most of the speakers (there are defo 2 speakers not amped up tho) and a little one powering the 2 subs and is 2 channel (i think its 100w one doin the subs)
the philips one has no adjustment on it so ive left that... but the little one doin the subs has gain (-2 to +2) crossover (on/off) and filter (high/low)
it was set up with gain +2, crossover off, filter high and the subs were facing the rear seats (was pushed up against the back too)
ive just changed it to: gain +2 (same) crossover on, filter low... also ive turned the subs around to theyre facing into the boot
is this right?
the sound is now more crisp, but i can barely hear the bass... its nowhere near as thumpy as it was unless you turn the bass right up on the headunit(which the normal speakers dont like too much)
is this right? should i put it back how it was? wahst the proper way of setting em up?