Hello guys,
for those who are playing with a ModPack that has Factorization in, here is the most awesome way to fully automate your reactor:
https://dl.dropbox.com/u/17885899/2013-03-15_17.01.14.png
I am using routers! Since you can set routers to pull in/out items from specific inventory slots, it is VERY easy to automate your reactor safely. Together with Applied Energistics (thats the weird cabeling above the routers) you can even fully automate it. If you dont have AE, routers will still make your life a lot easier.
I hope I was able to help a few of you, because i don't think anyone else came up with such a solution yet.
Thank you guys and keep up the good work!