Default SD Card File System Problems Flashing ROMs

I have flashed a CM11 unsuccesfully and today sucessfully flashed AOSP Kitkat. I have found the file system is screwing with my sdcard. I have emulated/o, emulated/legacy, SD0, and SD1. I always run a Nandroid before flashing and that completely disappeared from my internal storage, it was not in any of the directories.

Not only that but after I booted up only a few of my apps were restored by Google restore. I installed Titanium and it had nothing. It informed me that the phone ID had changed and asked me if I wanted to change back for compatibility. I let it do it and ended up with a Titanium backup from a couple phones ago.

What the hell is going on and what is the best way to deal with the storage file system after a flash when one has these extra directories? Can I merge? I'm afraid to delete one because I do not know that it will not have some data I might need.

Samsung Galaxy SIII T-Mo, stock rooted root_66
Asus Transformer TF-701t- not rooted yet