As far as a sub woofer, there are not a lot of options. It's going to involve some space. In my deliberations, I was at first intending to mount 2 subs ,one in each saddlebag facing the rear wheel. I instead went with the simpler route with the JL Audio micro sub and have been very happy with it.
As far as the amp, just depends on which amp you choose. The amp I used is pretty small in size and therefore can be tucked in a few places. The OEM location though didn't quite seem like a good fit. The amp by itself will fit but by the time you add in all the wiring it's a bit tight. Not to say it couldn't work, but the location in the left saddlebag where I put it, really takes up no usable space and it is easily accessed for any changes or adjustments. It could also be placed up in the fairing.