if you can do run of srb2 mods with SRB2 Net launcher, then do you use SRB2 Launcher for those runs too? (Edit: Same Goes For The music edit wads?)

You can use the SRB2 Net Launcher to play the game, too. That's perfectly fine. Basically all that matters is adding the WAD file into SRB2 so you can play it. You can achieve this through the command line (batch files) a launcher (Your launcher in this case) or by simply using the console to add them into the game.

It should be noted we don't want people to go crazy with mods and runs with mods in them, generally things that don't change the gameplay in anyway are fine but anything else is not allowed.

Thank You! (for Asking.) :)