URGH Permissions. -_-

Hey! I have been setting up a 1.6.2 Bukkit server. I have simple worlds, a great server so far. If only PERMISSIONS was easier! I have used PermissionsEx, GroupManager, and bPermissions. PEX was the only one working with the server. I had prefixes and everything, all groups set up. Then I restarted my server, took away GroupManager, and all of the PEX work I did was gone. Very confusing. Since then I have given up on permissions and just have been playing on my server and building. Then I think of "permissions!" and I try and try, then fail and fail. Please help 0.0