How do I setup permissions.yml correctly?

I`m currently running a standard bukkit server on Minecraft 1.12 with a fair amount of plugins installed such as mcore and mcfactions, I also have things such as worldedit and "simplewarps" installed on the server. I have absolutely no clue how to edit permissions so I leave the file blank and use mods that distribute permissions on its own. I just /op people that need access to a specific command and leave people unopped who don't (which is a horrible practice). I recently just moved over to a spigot server because I read somewhere that it could help me set up permissions, I then installed PermissionsEx, Vault, and ModifyWorld, but I still cant seem to figure out how to configure permissions.yml. What i`m trying to do is have all factions working for normal users (except /f admin of course) and I want worldedit to be completely restricted to ops/mods only. And I want my simplewarp plugin to be accessible to everyone because everyone keeps asking me to setup user create-able warps. Any advice?