Factory Stereo Problems

I was just given a pair of 10"s in a bandpass box with an amp. I ran into a problem when I decidied to get them installed. A person working at bestbuy said that my factory stereo was the mach460 and was a pain to add any aftermarket stereo equipment to. The guy then said they could wire it with a line out converter but it would sound like crap. I also realized to get the subs in the trunk the mach amp rack needs to be taken out and put back in after the sub box is installed because the box is to big to clear the mach460 amp rack. The box is about 14.5 inches tall and 14.5 inches in depth. And I know its possible to fit this box in the trunk because i have seen other people with non-mach stereos have this setup in their mustangs. Is anywon having any similar problems and can anywon tell me is there a way to get better sound out of my subs besides ripping out the whole mach system?
Any info would be much appreciated
Thanks

Figured this problem out finally thanks to help from a few of people.
1. The box has to be small enough to clear the amp rack
2. Bestbuy wires the line out converter in the wrong place. They wire it to the back of the head unit instead of the mach data cable located in the trunk.