I repeat:
http://www.vis.uni-stuttgart.de/~rose/stuff/fate/faq.html#faq2
You can move them into worldspawn (right-click -> move into worldspawn… or something like that… I cannot remember right now)
Once again… faq #2 is your friend:
http://www.vis.uni-stuttgart.de/~rose/stuff/fate/faq.html#faq2
Guess what? faq #2 
http://www.vis.uni-stuttgart.de/~rose/stuff/fate/faq.html#faq2
BTW: it is an alpha… I think I pretty clearly state at the website that texturing is VERY experimental at the moment. (Sorry if this sounds rude… but at the moment, unfortunately, you have to live with that incomplete implementation of texture support)
Did I already mention faq #2? Just in case:
http://www.vis.uni-stuttgart.de/~rose/stuff/fate/faq.html#faq2
BTW: If somebody wants to write down a more detailed guide how to get rid of the multi-layer brushes… feel free to do so… I will happily add it to faq2.
nice idea… maybe I will add that (if there is some space left in the GUI)
My hope is that with version 0.15 or 0.16 there won’t be any need to ever touch the terrain in Radiant again… The user should be able to texture the terrain with Dotproduct(2) and/or alpha volume blending in FATE… I also want to add the possibility to blend more than 2 textures by using multiple brush layers… and the user should be able to easily achieve this in FATE. I have a dream… 

