I can’t really help, because except for skins my install is ‘vanilla’.
If you have a clean backup, then go nuts - try both and see what works best for you? It doesn’t matter If you cock it up, in the worst case scenario you can always restart with a fresh install. Besides, I have learnt a lot more from my mistakes than from my successes.
Edit: A DCS essential (IMHO) is a very excellent utility by @SkateZilla - see this thread
Among all the other awesome things it does is have a very useful repair function… I have used that on more than one occasion 