There are a lot of permissions to choose from but i dont know which one to choose. Which one should i choose?
It depends.. I use PermissionsBukkit because that was the first out when SuperPerms was released and have never switched since. PEX and bPermissions are good choices as well. Personally, I think bPermissions is the way to go, and PermissionsBukkit is probably the hardest to figure out, out of those 3.
If you can't figure PermissionsBukkit out, switch to bPermissions. It's probably easier to figure out.