As a general rule, .lay/Layout files go in your Layouts Folder. These file can be for a couple of different things.
1. Layouts for mission building.
2. Layout created to be used with GSL Editor to insert GSL GOB's.
Several scenery developers, myself included have started to include these with their scenery. I include them for two puposes.
1. It allows Mission Builders to quickly populate an Airfield and then they just delete the items they don't want in the mission. They don't have to go through the process of placing and alligning AA Guns, Aircraft in revetments, etc. Those I call "Fully Loaded" Layouts.
2. Layouts of the GSL included in the scenery. If you wish to Add/Delete/Change the GSL for a GOB you just load the Layout in MB and make your changes. Then Save the new Layout and insert it with GSL Editor. I generally name these Layouts with the name of their respective GOB.
Hope this helps...