I have a 2001 Miata with the Bose system...bypassed everything for my install....i understand that the bose speakers at only 0.5 ohms so do not use them with an aftermarket amp

i have replaced them with Infinity separates and installed 2 amps in the trunk...one for the door speakers and one for the sub that i installed in the passenger side footwell

i stacked the amps on top of each other in the left side of the trunk but did not cover the small 'well' compartment under the antenna

i never had a problem with not enough storage space as i really only use the car locally

good luck!!