It depends if you want to install the V1.0 (-> data folder) or last nightly build (-> new directory structure)
It depends also on mods you want to install
I think (but I am not the best to give you an advice on this, as I'm back after a year) you should install the V1.0, as most of mods should be compliant, or propose a version compliant with V1.0
So, my advice is : as first step, keep it simple, install V1.0 (data folder) and check if it works