Keep your 1.09.4 files and 2.0 files in separate folders, as they're practically two different games. None of the stuff will work with each other with the exception of music wads, text scripts and the like.
A lot of stuff from 1.09.4 can be carried over to 2.0 if you put the effort into it, others can't. With levels, it's normally as simple as running level converter and making whatever other appropriate changes with a level editor. Most graphics can be ported just fine, but the 2.0 character system has less flexibility for customization in comparison to 1.09.4, so porting characters will probably force you to implement some painful nerfs into it. You'll have to recreate socs completely by hand, as there's pretty much no consistency between the two versions in that field.