A 6.5 " sub will fit perfectly in the right side saddlebag. You could also get one in the left bag, but some more work needed in there as the same area in the left side is not flat. Here is a pic of someone who mounted 8" JL audio W3 apekaers.
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These required some fiberglass work though. I had originally thought of doing the same, but wanted to try out the 6.5" as they are a much easier fit and the one's I've heard from JL Audio and Digital Designs really put out some tremendous bass. I have decided to try out the engineered enclosure with the JL Audio driver first. It will be easily removable. Like how long it take you to open the bag essentially, if I need the space for a trip.