You don't really bypass the factory Bose, more like use it. Clip the two wires running to the sub in the spare tire and connect them to a crossover and then to your sub amp. I don't remember the thread off of the top of my head, but there is one that tells you what to do. If there isn't, PM me and I'll take some pictures and tell/show you what to do. Good luck!
-Brett
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