I'm not 100% sure of what you are trying to accomplish, if you are making an effort at keeping the skins generic or if you are making squadron-specific skins.
If you are doing the skins as squadron specific, then you might try to unify as much information on each decal as you can. MyTai01 back in the days of SFP1, created an excellent decal map for the Thirdwire F-4. Have a look at some of his work for some good examples of how to combine multiple graphics onto one decal specifically for this jet. You should then be able to accomplish a lot of jet-specific markings while saving space on both your decal layout and HD.
If you are attempting to keep the skins generic so that they can be used by any squadron... well that's a totally different story. I wish that TK had expanded the decal levels so that certain levels might look at 2 variables (such as aircraft number AND squadron number) or even 3 (aircraft number and squadron number and carrier number) instead of just 1. As it is, his system is still one of the best for creating excellent skins and getting some good BuNo-specific markings.
Good luck. I am as much a Phantom Phile as I am a Tomcat lover, so I look forward to whatever you create.