sound settings are usually not really sound issues but are FPS issues. the game starts to run roughly, fps jumps around, and so sound gets affected. Turn on your FPS and watch to see what happens - if fps becomes inconsistent, sounds will be also. Recommendation - turn on framelimiter AND frameskip. That will help, but may not fix the issue. May need spusync, which requires restarting FPSE.
PS3 controller - Someone posted in another thread (can't remember where) about being able to use the PS3 controller. I don't remember if they said it would work with FPSE or not. If the controller works with your device (just in general, you plug it in and your device recognizes it / can use it), it should work with FPSE - you should be able to map the buttons to hardware buttons.