Put them in the trunk. You can make some panels on the side and flush mount them for a nice clean look and you'll still retain most of your trunk space. A few people on here have done this and there are some pics floating around.

Vinny 2000 T-RED CSVT MODS: 18" REV model 2 ST200 struts/Roush springs CTA intake Pipe/K&N Filter Dtec Heatshield Optimized TB True Duals w/ magnaflow mufflers/resonators