If you have the drive space you can take your modified version of the mod and copy the directory to another name, like FirstStrike_internal or something. Then either reinstall the mod or change it back (in the original FirstStrike folder). After that copy that directory to a folder called FirstStrike_Online.
From there a simple batch file can delete the FirstStrike folder and copy whichever version you want to use to that name. Make sure any changes you do in your custom map are saved back over your copy before restoring the online game.
This is how I have it set up for testing, and again you need the drive space to do it.