Mod Organizer from what I have read isn't really working properly yet, but it is the better mod manager. I was using it to mod vanilla Skyrim, it's much better at managing more complicated mod lists that have a lot of overlap. Also from what I have read, the author of MO is teamed up with the NMM guys now so that may eliminate MO all together.
Yeah ELFX was awesome, I used that with ELE for vanilla. Hopefully it gets ported soon but for now I will be using RLO, it has come along really nicely since the vanilla version.