This is a nice feature, though a bit hidden.
First you make a copy of the "f9h_large_fairing.cfg" for your mission, here "f9h_large_fairing_SR.cfg"
In this new cfg-file, you change the path to the fairing texture, like
FairingTex = FalconHeavy/f9_fair_logo_large_SR.dds
You can copy the...