FSX will display the airport that has the highest priority in the scenery library.  You can make a new folder in your FSX root folder and call it Addon AP Scenery or whatever.  Inside that folder you need another folder called scenery and if the scenery you are adding has a texture folder then you will also need a texture folder in the Addon AP Scenery folder.

You install KSAN per the directions that came with the airport, but instead of installing to Addon Scenery you install it to Addon AP Scenery and in your scenery library you put Addon AP Scenery above your MSX So Cal scenery and above the default Addon Scenery folder.  Now FSX will display the new KSAN rather than the MSX So Cal KSAN.

If the KSAN you are using has its own KSAN folder and inside that are scenery and texture folders then you can make a folder called Addon AP Folders in your root FSX folder and put the KSAN folder in that, then just add KSAN to the scenery library, make sure it is above MSX So Cal and Addon Scenery.