The choice is yours and what your needs are.
If you plan to run only a few mods that do not conflict with each other then OBMM is fine.
If you plan to run a lot of mods and want great conflict reports and ability to solve them without serial reinstalling then BAIN is the way to go. I'm of the mind that BAIN is superior, but then again I'm biased.
If you have already mastered basic use of Wrye Bash and are going to need it then all the more reason to install with it too.
I still use OBMM for omods with good scripting and few conflcits (like TheNiceOne mods) and for shader based mods. I also still install OBSE plugins with it - though BAIN can do that now too. OBMM also can handle bsa unpacking-repacking too (BAIN cannot).
So you don't have to choose and use both, but for the bulk and for the mods that do conflict I'd stick with BAIN.
I wrote http://www.gamesas.com/index.php?/topic/1084204-bain-mod-installation-projects/ about it too.