Remote control issues

I have the Polk 9500BT, I've got several questions.
1. How do I stop my other remotes from interacting with the Sound Bar. For example if the sound bar is on and I turn the tv off, the sound bar changes the source, or if I try to use my Android box remote it changes the source on the sound bar.
2. Why does my Sub seem to kick in and out, especially noticable when listening to music

Answers