One of the things that bothers me is that whenever I put the visuals on random and timeout and I unplug the empeg, i lose that setting. What I want to do is make it so that I can press two buttons on the remote so that those features are turned on. Basically since I don't have a tuner I want that button to do the commands. Short press and random is turned on, and long press and timeout mode is selected. Is this even possible? I didn't see anything in FAQ about this.

Known bugs that are planned for a fix in the next release don't usually get put in the FAQ, as I'd just have to delete them again when the new release came out.

Yes, you can remap the Tuner button to do (whatever) you want it to do. Install Hijack, and peruse the button-remapping information for Hijack.

Cheers