Bungeecord Permissions

So I already run a server but with donations coming in I wanted to do a little better for the players. I figure I would spend a little time with bungeecord. The biggest issue I have found in my research is permissions. I guess my question then becomes whats the best plugin to manage my permissions bungee/network wide? Or would it better to use say groupmanager or whatever perms plugin on each server individually?

*edit*I suppose the better question is what is the best way to do permissions on a bungee server.*edit*