Sorry you are having issues but with my amp slipping loose from the saddlebag, cocking sideways and rubbing a hole in the bag, the only solution the MoCo offered was a new bag and mounting it the same way again....double sided tape. I looked at many different options to go with when the tape gave away again with this new bag but so far, it's stayed in place after 1 1/2 years. Guess they cleaned the surface this time and used better tape. The mounting hardware around the amp had a "rest" made into the saddlebag to help keep it in place but using double sided tape in the first place is pretty lame, IMO. It's way to heavy an object for that.
Watch using the velcro. It may allow for the amp to vibrate more.
Really, there are only two options. One, the MoCo should have designed the saddlebags with a better mount for the amp with maybe a rest on both sides of the bag instead of just one side. The other option is to keep all the amps under the faring with just wire running to the speaker and the iPod connector. I like the second option as it would help with the weight issue in the left bag. Quite a few of our group have gone aftermarket and done the amp relocation route. If it happens again (tape releasing grip...and I keep a good eye on it) I won't have the warranty to help me so the amp will be removed and the under faring route chosen.
The MoCo stated in my resolution that this was the first time this had happened. I kinda doubt that but hey, they got me a new bag within a week and covered it (as they should have).
Good luck in whatever option you decide to take with your problem.