The BF2_Modtools? It should be a folder called BF2_Modtools, which contains everything you need, and it should be in C:\, your root hard drive folder. The program that is ran by the shortcut in the start menu creates new maps. The BF2_Modtools.exe inside the BF2_Modtools folder is a debug version of BF, you put that in the gamedata folder.
I bet someone will come by and just tell you to go to www.gametoast.com
, which is more devoted to modding and will give you a better answer.