Some cable manufacturers make a very thin/flat cable specifically for being run under carpet...Monster is one option. You can go to home depot or menards, etc and buy a cable fishing tool to help pull it under the carpet. They're only about $10, I think. You can use this combo without having to pull back the carpet, just make sure you go under the pad too & don't let the cable twist.
Klein Tools Depthfinder 25 ft. Steel Fish Tape - 56005 at The Home Depot
Amazon.com: Acoustic Research PR361 Speaker Cable, Flat 16 AWG, (50 ft spool): Electronics
I wouldn't buy anything monster, it's way overpriced, just my opinion. Myself and several others I know have had very good luck with monoprice.com. Lot's of options and every cable I've ever ordered from speaker wire to 50' HDMI cable all have been cheap and high quality.
I recently hid my sound system in my hall closet and ran the back speakers down into the basement, under the floor joists, and back up again, just like several others have suggested.
Good Luck!