Thank you for including me in this discussion, I can only tell you what I do and that may not be best practice.
My cab has also been set up for a long time and I've always used MAME standalone because I have my controls set and all my ini files, shaders, art work and bezels set up. I won't be using RetroArch for that.
I do use RetroArch and it is set up for a lot of the console systems like SNES, Genesis, because it's initially easy and I love the Mega Bezel reflection shader and scanlines. What I don't like is, it can be complicated to set up on a deeper level, especially controls which I need a reminder on. I have controls working but it's a mystery how. It is nice having everything under one roof and it will be the go to emu for HS2.
For the main computer systems e.g. C64, Spectrum, Amiga I use the standalone emu although they are not great on a cab. I can never remember the button shortcuts and so I just rely on my Rii mini keyboard to load saves etc.
Most important thing is, have a backup, have fun and ask for help instead of getting frustrated.