I love C & C, personally. I use it with a bunch of other mods, including the big ones that it really seems to conflict with: Realistic Fatigue and Enhanced Economy. Here's the thing about it: the mage's guild part of the mod works. No problems, period. The fighter's guild exam system is the part of the mod that can give problems and it seems to be related to the spell timer not firing correctly. So here's what I do:
1. Use it.
2. ALWAYS make a regular save (not a quick or auto save) before I talk to the examiner to take a test.
3. Take off my Inventory-is-a-backpack pack and set it someplace safe so I don't lose my inventory, if that's applicable.
4. Take the test. If the spell system/script fails at any point (and it does a little less than half the time), reload the save and try again. I've never had to reload more than twice for it to work properly.
5. Once I have my diploma, save again. Exit and reload, to reinitialize enhanced economy.
Works for me.
As for the quest markers, I never noticed it before you mentioned it. Unless I'm mistaken, all it does is make them togglable via the cobl options menu.