Golden Sun is completely different. What you need to do is find the loader for the palettes and have it load 256 colors. Then, you need to insert 256 color OWs and make sure the game reads them as such.
1) I only use the registers and instructions screens. The others are just extras.
2) Trace is the same, except that it will follow bls. Run next won't.
3) It doesn't run everything, only the stuff it needs. So, if you set a breakpoint on a routine, that routine actually has to run for it to activate the breakpoint. Ideally, you should know what you are looking for, so you will know if the routine is called. So, if you are trying to find the OW loaders, you would set the break, then warp. If the break point doesn't activate, that wasn't the right routine.
4) Ahh, maybe it skipped over it. The game likes to do this:
got it? Most code has a section in it that only runs if there is an error or other issue.
5) Umm, besides breaking on instructions, you can also break on ram changes and such. Look in the NO$ debugging documentation for info on how to do that.