Just copy the folder that contains your airport and save it under another name. Place the new folder in the Custom Scenery folder in X Plane.
You can disable either or both of those custom versions by changing the line in the scenery_packs.ini in the Custom Scenery folder as listed below for my KPUJ scenery. You can also see that I have disabled the hd_global and treeline sceneries as I'm trying to get my framerate up. :(
I 1000 version SCENERY
SCENERY_PACK Custom Scenery/Aerosoft - EBBR Brussels/ SCENERY_PACK Custom Scenery/Aerosoft - EDDF Frankfurt/ SCENERY_PACK Custom Scenery/Aerosoft - EDDK Cologne/ SCENERY_PACK Custom Scenery/Aerosoft - EDDM Munich/ SCENERY_PACK Custom Scenery/Aerosoft - EDDS Stuttgart/ SCENERY_PACK Custom Scenery/Aerosoft - EDDT Berlin Tegel/ SCENERY_PACK Custom Scenery/Aerosoft - EDLP Paderborn-Lippstadt/ SCENERY_PACK Custom Scenery/Aerosoft - EGBB Birmingham/ SCENERY_PACK Custom Scenery/Aerosoft - EGKK London-Gatwick/ SCENERY_PACK Custom Scenery/Aerosoft - EGLL Heathrow/ SCENERY_PACK Custom Scenery/Aerosoft - EGPF Glasgow/ SCENERY_PACK Custom Scenery/Aerosoft - EGSS London-Stansted/ SCENERY_PACK Custom Scenery/Aerosoft - EIDW Dublin/ SCENERY_PACK Custom Scenery/Aerosoft - LEBL Barcelona/ SCENERY_PACK Custom Scenery/Aerosoft - LEMD Madrid/ SCENERY_PACK Custom Scenery/Aerosoft - LFMN Nice Cote d Azur X/ SCENERY_PACK Custom Scenery/Aerosoft - LFPG Paris CDG/ SCENERY_PACK Custom Scenery/Aerosoft - LFPO Paris Orly/ SCENERY_PACK Custom Scenery/Aerosoft - LPFR Faro/ SCENERY_PACK Custom Scenery/Aerosoft - LSGG Genf/ SCENERY_PACK Custom Scenery/Airport_KPUJ_Paulding_Northwest_Atlanta_Custom/ SCENERY_PACK_DISABLED Custom Scenery/Airport_KPUJ_Paulding_Northwest_Atlanta_Lego/ SCENERY_PACK Custom Scenery/Airport_KVPC_Cartersville/ SCENERY_PACK Custom Scenery/KCOI Merritt Island/ SCENERY_PACK Custom Scenery/KMLB Melbourne/ SCENERY_PACK Custom Scenery/Global Airports/ SCENERY_PACK Custom Scenery/KSEA Demo Area/ SCENERY_PACK Custom Scenery/KSEA Demo Terrain/ SCENERY_PACK Custom Scenery/LOWI Demo Area/ SCENERY_PACK Custom Scenery/My Library/ SCENERY_PACK Custom Scenery/OpenSceneryX/ SCENERY_PACK Custom Scenery/ff_library/ SCENERY_PACK_DISABLED Custom Scenery/zzz_Treelines_Farms_North_America_v2/ SCENERY_PACK_DISABLED Custom Scenery/zzz_hd_global_scenery3/
As you can see, I have two versions of a local airport, KPUJ, that I am working on. A lego version for the Scenery Gateway which BTW has been uploaded to the Gateway, and a custom version for which I am modeling a more accurate representation. You'll notice that at the moment, I have the lego version disabled, so when X Plane loads, my more accurate version is what gets loaded. All you have to do is open the scenery_packs.ini with notepad and disable/enable the scenery you want X Plane to load at start up. Make sure to save the scenery_packs.ini after making you entries.
Hope this helps