ok this is what u do, just COPY your maps folder our of halo and paste it on ur desktop, never change that folder or apply any mods to it, just copy maps out of it when u want the regular maps back. as for mods, it depends, if the mods are ppf files then u need ppfomatic, just go to the downloads section it will be in there. if they are just files like .map then all u have to do is replace a map in your real maps folder with it. if it comes with objs then u have to use halo map tools 3 (also in download section) and go to pc models and scroll to that name in the list at the level the mod is for and import that obj in for that model. if they are dds files then do the same thing but in the bitmaps section of that level.
ur gonna have all ur backups, but NEVER put things into them they are there to not change, but for bimaps and sounds ppfs just apply those to the bitmaps.map and the sound.map not maps like bloodgulch.map