The custom maps on aa.com are all checked first (most of the time) before they are put on the server for the public. They should not slow your system down any more then a stock map, and they will not affect your single player game either. Just make sure you know that the map has been tested before you download them, so you know if there are any bugs. If you go to the servers website, you will get a list of what maps are currently in the rotation. You can then donwload the ones you need. If you use All Seeing Eye or Gamespy, it lists what map is currently being used in the game.
For the aa.com's server, go to
http://mohaa.xgshosting.com
When you down;oad the PK3 file, it goes in your MOHAA/Main folder, and that's it.