When starting the game to edit it always choose to be the very first civilisation on the list (at the top) that way you will have a chance to edit the map before anyone takes their turn. As long as no turns have taken place you will be able to use the worldbuilder to edit it, save it, quit, then relaunch it as a new game (and edit some more if you need to).
If you want the file you'll find it in your...my documents/my games/warlords/saves/worldbuilder folder.
For vanilla civ replace the 'Warlords' references with 'sid meier's civilisation 4' but it's the same process.
You can't launch multiple mods simultaneously.
Merging is tricky but there are already many pre-merged mods in the forums.