S3 Bose System

A proud owner of a 2000 S3 - which came with a Bose Concert system - god I have never heard such garbage in my life - bass and treble turned up and it sounded like a £50 stereo from Halfords.

I binned it (not literally) and invested in a Pioneer AVIC-X1 - sat nav amongst many other toys - and using the various tools within this system improved the sound in the car by 100%

I then went mad and replaced the front bose speakers (I think the tweeters are made by someone else couldnt see logo on it) with some infinity components - and sound improved yet again

Having another bout of ebayitis I then invested in a custom made shelf and slipped a pair of 6x9's - I disconnected the speakers from from the back of the car and connected the new 6x9s - but I'm not getting any pounding bass from them -

Is this because the bose bass box all the speakers are connected to the bass box - and all the bass frequencies are taken out of the input into the speakers around the car?? If this is the case.... any way to by pass this and let the infinity's looose?