I'm a little bit confused about how to properly use GSX with various add-ons. Fenix, PMDG, etc. Have the ability to call for services in the EFB and in the FMC/MCDU.

How do I know whether to use the EFB, the FMC/MCDU or the GSX Pro menu?

I may be wrong, but I think GSX only does the visuals of any loading process. To get the aircraft correctly loaded with fuel, PAX or cargo you're always going to have to use the EFB etc. as well. External addons (like BATC) can inter-react with GSX and trigger certain GSX operations but, again, they won't change anything in the actual aircraft payload. At least that's the way I think it works - and I'm open to be corrected (!).

easy way to tell if you have to use the efb on aircraft is that if you try to open gsx thru the menu, and it says remote control than you have to use the gsx interaction thru the efb with the fenix. With fsl labs version it either the efb or mdcu, same with the ini build 350 its thru the nd display. with loading the aircraft with fuel it does load the aircraft using gsx