I don't really understand what you mean. But, I'll try to answer it tho. I'd recommend Factions for a PVP server (although you can turn off the PVP features). It's quite easy to setup, as well as to use. Towny is great for more Survival aimed servers. It's quite hard to learn/setup, but worth it. I've got both on my server, and it seems to work well tho. It's more of a test.
Ah, that's completely different. I explained this in my PermissionsEX FAQ. You can find this here: http://forums.bukkit.org/threads/permissionsex-faq.96153/
That doesn't help if you have more than one rank in your faction. (Because multiple prefixes aren't supported by PEX)