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I hooked up my bose sparetire sub to a Alpine M200 I got off ebay for $70ish and it hits very well coupled with aura bass shakers in the seats. This mod lets you keep your trunk space.
You can dink with the built in amp but it really is low power and has an annoying on/off popping sound in between songs that is a pain to troubleshoot. I was planning on putting a Jl audio 6W0 sub to replace the bose driver and use the enclosure but I found the alpine amp drives the bose to as loud as I need it.
Here's the tool kit to the left, amp behind the foam, and sparetire with sub