Playing in the EPL, I've edited the game using FMRTE to add Continents>World to the European Union, and to be treated as non-foreign. However, I am still limited by the work permit system. Is there a way for me to edit the game so every club can sign players from wherever they want without the limits of work permits, or do I need to start a new save and use the pre-game editor to set this up? And yes, I know I can just add an EU nationality to a player to get around the work permit system, but I don't want that advantage over other clubs, so I want to remove work permits for everyone. 

This is already covered in the FAQs which can be found on the homepage.

Why use a pre game editor ?

Just edit the player you bought to second nationality English right before he joins your club and viola .... job done. No poblem with work permit anymore.