Problems with the permissions on my site

I have installed two plugins. A directory plugin called Connections and a classified plugin called Another WordPress Classified Plugin. Those two plugins have an edit button on the frontend that takes the user to a specific menu in the backend. The user will only see those two menus and not all the other. It should work if my users are subscribers, and they all are. But all the other menus are still showing in my dashboard. I have tried plugins like admin menu editor, user access manager and adminimize, but even if I disable the other menus, so my users should not see them, they can still see them all. I think for a couple of months ago I had some troubles with the permissions, and then I was messing around with the different read and write permissions in my file manager in my cpanel. Am I right, that there are two kind of numbers that sets the permission? Are they not something like 644 and 755? I can see the numbers in my cpanel. But I dont know what files they should be with. In my wp-content folder, I can also see these numbers. Do you guys think that it has something with my permission to do? I have tried to de-activate my plugins, but it still dont work. Can you say what the permission numbers are for my users or folders in my cpanel? I really hope you can help.