First off, The location of the sub as selected by eclipse/attitude is purely for ease, and not performance. No audio person would put that sub in an oversized, exterior ported "enclosure".
I left the stock system as is. I purchased a 5 channel class D amp (Rockford F), and a eq which allows two inputs. One input is from the cheap stock head unit, and the other is for an iPhone or what ever I choose. I wired an outlet for the sub inside the TH for use when watching a movie or radio inside. I use the stock speakers plus the sub. The addition of a quality amp and sub improve the overall sound quality inside. The eq allows for adjustment of the sub volume.
The same sub can be taken outside and wired to a 5 channel outside speaker outlet box (FL,FR,RL, RR, and sub). I have 4 additional kicker enclosed speakers for outdoor use (boon docking) or concert type events.
This whole system was purchased for under $600