Firstly learn the distinction between a faction, and a guild. A faction in the CK is basically just a way for you to group NPCs together in order for them to share behaviours, dialogue, radiant story quests, etc etc. So the Bears in Skyrim are in a faction, not a guild 
Now you create a Guild by putting people into the same faction. And if you want a hierarchy, that's where faction ranks come in. Pick how many ranks you want (my guild has about 8) and give them each a name. As far as I know though, that name is purely for a CK viewer and means nothing in-game; it's the faction rank number that's important. When you've got the basic framework of your faction set up, then you can start creating NPCs and putting them into the faction (factions tab in Actor window) and setting their rank accordingly.
Next comes quests. You set up which "rank" or NPC can give various quests, set up dialogue to be specific to your faction and/or the ranks in your faction.
After that, you've basically got your Guild
Just need to add the cosmetics of it for the player to experience.