When you first open AFCAD it will be blank just click on the open airport and it will load up all of your active airports  you can then enter the ICAO or use the menu to select the region/state/city/than the airport you want to open. After your airport is open you can than make any changes you want and than save your work. I would suggest you save any AFCAD files in a folder called AFCAD or whatever you like in the ADDON SCENERY FOLDER. Rember you will have to activate the scenery using the add scenery tab or it will not show up.
Just make a folder called AFCAD and then a folder within AFCAD called scenery and put all of your afcad files here. That way any other files you add will be generated when you start up FS.