Ok, it works. I suggest you to put Coldbird's FTP for VITA in your console (inside NPEG00020DATA01) and install it. It's very useful.
Remember to turn on the wifi when you use it and that if you leave it there without doing nothing for some minutes at all it shuts down.
Playing Gungnir with a couple of cwcheats activated and I have no problems at all.
You have just to get used to how things works on the Vita (structure for the homebrews, where they go, names in caps (extensions too!!), max 8 characters, and so on...).
If, when you move a folder from pc to the root of the ms you don't see it, just close the ftp connection on pc, close the program (i use filezilla), start it again and connect to the Vita ftp again and it should be there.
Or just create a new folder on the root of the ms, rename it (seplugins for example) and just put the contents in it from the folder on your pc.