First of all, welcome to GT!
Now, a definition of the word munge.
Munge: verb
A BF2 modding term meaning to compile your map into a format which Star Wars BattleFront 2 can use to show the appropriate effects, terrain, and objects as you have directed in Zeroeditor, your sides, and also your LUA scripts.
lol that was kind of fun.
When you want to make a new map you have to go into BF2_ModTools\data\_BUILD and double click on
Modtools VisualMunge.exe and then select your game modes you want in your map. Then click munge.
Seriously though you should read the Getting Started doc in BF2_ModTools\documentation. This is all explained in that document.