Bukkit perms for Minecraft?

I'm new to this and they're kicking my but.

I have a hosted server 1.7.2 with Bukkit and a long list of available plug-ins. I've tried three simple ones, Hug, EasyFireworks, and PermissionsEx. The jars are in the plugins folder and I've seen them load successfully on reboot. But the only config files are in the jars, not outside, and no command I give does anything.

I must be missing something basic here, permissions is my guess. I'm OP so it seems they should work or at least give me an error message but I get nothing at all. Command not found.

I don't even know the questions to ask so I hope you can all help me out. If I can figure out a few simple ones the others won't seem so intimidating.

Try reading the dokumentation of PermissionsEX. I'm pretty sure that the OP gets deactivated when the Perms are activated, meaning that you need to configure the Perms and make you admin so you can use all the commands.
Each prugin that is compatible with Perms should have a list somewhere of the useable perms, meaning that if you want to add them you need to use the listed perms, and not something other. Also: Never forget that the "tabulator" is a no-go when making perms.
Making permissions can take its time, it took a few months for me to fully understand the system they where built with.

Also, the.jar should extract a folder with diverse config files when loaded successfully, but i don't know if they have changed this since i last made a Bukkit-server…