The ones in the trunk will work, but you would need to either get the stock shaker 1000 amps, or run them off of the 500 amps. If you choose to use the 500 amps, they will sound like poo. Best bet is to use the factory 1000 or install a new amp.
If you want my opinion. I would ditch the shaker for a new HU, then install the 1000 sub in trunk with its own amp. The cost is more but the sound quality is 4000% better. Ask away, I will help the best I can.