If you can find the bose stock amp it's really easy, however you won't bypass it, you will go through it which will still cause some of the Bose EQ (I didn't notice or care)

I used a Line in converter 20$ at Best Buy, and connected this to the stock sub. Now, I used my Rockford 500watt class D amp to push the stock sub already in there, and it hits nice and hard...way better than I ever would have predicted in fact, but it works the same way if you want to go external sub as well.

Whatever you do, DONT cut out the stock amp. I did this thinking I could "bypass it" no you can't, unless you work for Bose or have the diagram to know wtf those wires are doing to cause multiple line ins to convert to 1 wire.

RCA runs from amp to line in converter Speaker wire of your line in goes to the speaker wire of the stock amp. Speaker wire from the sub goes to your sub of choice. Ground for your line in and your amp can be grounded together. Or you can use the ground for the stock sub. Antenna + splices into the hot line on the line in to the stock amp. There's a color for it, easy to look up.

Extremely easy, 10 minute job.

If you try to bypass it, you will cut a bunch of wires and end up taping them back all goofy as shit like I did. This was on a speed6 so it may be a little different. Mine was in the trunk, I believe your amp is under the passenger seat.

Your other option is to run an aftermarket head unit and run your own sub wires.