You'll need to transfer files using Vitashell, maybe also Molecularshell will work, but I didn't try. Vitashell is something like "the unsure and unlocked version of Molecularshell", with it you have access to files which you should not touch.
That being said, you can transfer through USB the files, and actually there is no specific need for a precise location where to put them.
Vitashell (or Molecularshell) is able to install a vpk from every place on your PSVita, so you just have to place it somewhere, install it through the shell, then you can delete it.
Roms instead need to be where you can access them easely, I am not sure if Vitashell has a default dir, but you can set that inside RetroArch's UI. I've placed them in data/ROMS/ inside which there are the folders for every console, and inside those the actual roms or isos. The place where you can set the default dir is this one:
I did set it into ur0 (which is not the SD) to use the extra space inside the console itself. Not something recomended by some people, but I yet didn't find that this was the cause of any issues.
Then you can find them through the "Load Content" voice, or you can create playlists, but I am not sure about how to do it. You can scan the directories to find roms that will be automatically sorted by console in the main menu, but I did find this system to not completely work. Some games still didn't manage to get into that list, I don't know why.