I have different build configurations (Debug, Stage, Prod) defined for my app and I use User-Defined build settings:
to set up Facebook log
I put two files with the (same) name GoogleService-Info.plist into my project.
One is at the root and one is in a folder called 'staging', so as to avoid a naming conflict in the file system.
Including one in one target and the other in another makes it so that each target has a unique plist file with the correct name.