To mod this game, all you need to do is follow these simple steps.
1) If doing something for campaign, then all the data is in base.wz (which is a zip file)
2) if doing something for multiplayer (and skirmish) then all the data is in mp.wz (which is a zip file)
3) The best way to handle either case is to unzip whatever you picked above to another directory someplace, and play with it there.
4) Once done playing with it, you can then zip it back up exactly* like it was before, and then name it something.wz
5) take something.wz and put it into your mod folder and start the game with --mod=something.wz
6) you now have a mod.
7) No, you can't have a mod loaded, and try to join a game that doesn't have the same mod, it will kick you.
Note, I highly suggest you DON'T mix maps with mods at this time. While it may currently work, that will not be the case for future builds.
*While in this case, I said exactly, in truth, you can just archive what you need, just make sure the directory structure is exactly the same on the things you modified, or it will not work.