1. If you setforceOfficialBukkitPerm to true in the config file, it will only use Bukkit Perm.
2. PermissionsEX have all priority : http://forums.bukkit.org/threads/admn-dev-permissionsex-pex-v1-13-tomorrow-is-today-1000.18140/
3. If not found: Search for Essentials GroupManager: http://dev.bukkit.org/server-mods/groupmanager/
4. Look for Permissions Plugins (made by Nijikokun, TheYeti and rcjrrjcr) :http://forums.bukkit.org/threads/admn-dev-permissions-3-1-6-the-plugin-of-tomorrow-935.18430/
5. Look for bPrmissions http://dev.bukkit.org/server-mods/bpermissions/
6. If not found, fallback to Bukkit Official Permission System :http://forums.bukkit.org/threads/ad...-0-official-default-groups-plugin-1000.26785/
7. No Permissions set ? Fallback to OP (ops.txt)

Click here for easy copy'n'paste for permissions(Includes PermissionsEx, PermissionsBukkit, and Permissions 3.x).

You don't want to add every permissions to one of your moderator, but you don't want also to add them one by one. Then you'll use the node admincmd.* that give all permissions. And then delete every permissions you don't want him to have (by example the server permissions) admincmd.server.*.

pex.yml

groups:
    default:
        default: true
        permissions:
        - modifyworld.*
    Moderator:
        prefix: '&0(&Mod&0)&7 '
        permissions:
        - -admincmd.server.*
        - admincmd.*
users:
    TestMod:
        group:
        - Moderator

As you can see I added the minus (-) node (-admincmd.server.*) BEFORE the “total” node (admincmd.*) it's really IMPORTANT else it will not work.

In case of you want to use the ImmunitySystem it's the same idea for the node : -admincmd.immunityLvl.samelvl this node disable the need to have the same immunityLvl to do a command on an other player. Like for the server node, you have to put it BEFORE the “total” node.

pBukkit.yml

users:
    TestMod:
        permissions:
        groups:
        - Moderator
groups:
    default:
        permissions:
            permissions.build: true
    Moderator:
        permissions:
            admincmd.*: true
            admincmd.server.*: false
        inheritance:
        - default

Here the order has no importance, only the true/false count.

To learn how to set limits with permission plugins it's here : limits