Probably an easy question but something I've been having issues with... I only just started playing with the construction kit.

Basically, trying to get rid of Aela's tattoo/facepaint. I go into CK, find the right Actor, go into the adjustable menus for changing the facegen and the other features... Disable the paint. Look at the head preview: Looks clean. Save it as a mod, enable it. Then look at Aela again - nope, no changes.

I mean, I dont get why this happens. I altered the Dremora Merchant the Dragonborn DLC has successfully, changed his race into an Imperial and gave him a screwed up ugly face, even succeeded in changing his armor into Thalmor stuff... But no changing warpaint?

You might be having the bug that involves npc faces being messed up. Try this:
http://www.youtube.com/watch?v=rOXF89QtgYM