I'm not sure how close your shaker 500 is to my 2012, but here is what I did.
I removed the stock amp for the door 8" subs located on the drivers side panel to the left of the dash. I replaced this with a 200W Sony XM-4S. I am driving the amp using it's speaker level inputs with wires from the rear speakers. I installed the Shelby Kicker 8" subs in the doors to replace the factory subs.
I replaced the factory 6x8 speakers with Pioneers. This made a huge improvement in the sound. While it does not have the level of base that will make your ears bleed like a good set of subs, It has really good base and good clean mids and highs and I have the whole trunk free.
Shelby has a "canned" solution here: http://www.shelbystore.com/product-p/kic-s.htm
The sub Shelby uses in the trunk is fitted to the side, so it doesn't take up much room.
The bad thing about trunk subs in my experience, mine never sounded very good with the truck full. I had a removable sub in a previous Stang, sounded great, but I had to plan ahead and take it out before I needed to carry stuff.