Commander is not a mod but an external tool, so it doesn't have some of the problems inherent with installing mods. Some of its functions (like ship names) only take effect after the patrol is over. There may be a problem with functions that actually change game parameters. Personally I would go ahead and install it, but don't change anything until you end the patrol.
JScones will certainly see this thread and tell you absolutely what to do and not to do.
Any sound or graphics mods will be compatible with any supermod. Just be wary of anything that changes the AI sensors. It might be better if you use this thread to ask about any individual mods your are thinking of installing. I personally have a bunch of mods installed over GWX, with no problems, and Jimbuna, the GWX Chief Of the Boat, has a lot more than that.
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