Bungee Cord Permission Question

Hi,

This is just a general question. I was wondering how larger Bungee style networks work their permissions etc. and link it in with Buycraft or other stores. Do they use plugins like PEX or SQL? I have tried a few bungee networks before, but never been able to sync ranks across all the servers and link that to Buycraft.

I'm not trying to do it at the moment, I was just wondering how it's done.

Thanks