This is less of a tutorial, and more of an FYI. When I set up my SD2Vita, I simply copied the entire contents of my 8gb Sony memory card to my SD2Vita. The problem with that was having the same games on both cards.
This should be a simple fix for you and shouldn't require NoNPDRM for games you own legitimately.
Once you have set up your SD2Vita, edit your storage_config.txt file so that the location you want to delete games from is mounted as ux0 and reboot.
Next, simply delete all the games you don't want duplicates of.
Edit your storage_config.txt again to mount the location of where you wanted to keep your games to ux0 and reboot your Vita again.
Once you've loaded your CFW, open VitaShell, press triangle, and choose "Refresh live area."
If you've got the right source mounted as ux0, all the games' bubbles that you just deleted should reappear.
Now you don't have to worry about wasted space or which save is the current one on games that your memory card and SD2Vita share.

 

[duwen]

Yeah, it's a simple fix, but it's not very well documented anywhere.
When I did mine I moved all my legit games to my sd2vita and deleted them all from my 4gb memcard, but I left all the dlc for my legit card games on the memcard (and didn't duplicate it to the sd2vita). I did this because I still wanted to be able to use my legit game cards - so my vita is set up so that the memcard is ux0 if the sd2vita isn't inserted (and sd2vita is ux0 if it is inserted), meaning that if I don't launch h-encore it behaves like a normal/unhacked device.
This was a tricky config to get my head around, and again isn't well documented anywhere. Most setups seem to just presume that you're okay with losing legit gamecard functionality when you use sd2vita.

 

[CocoLove]

Yeah, it's a simple fix, but it's not very well documented anywhere.
When I did mine I moved all my legit games to my sd2vita and deleted them all from my 4gb memcard, but I left all the dlc for my legit card games on the memcard (and didn't duplicate it to the sd2vita). I did this because I still wanted to be able to use my legit game cards - so my vita is set up so that the memcard is ux0 if the sd2vita isn't inserted (and sd2vita is ux0 if it is inserted), meaning that if I don't launch h-encore it behaves like a normal/unhacked device.
This was a tricky config to get my head around, and again isn't well documented anywhere. Most setups seem to just presume that you're okay with losing legit gamecard functionality when you use sd2vita.

This is the issue I'm having right now. I don't want to waste space on my new SD card. I only have 32GB on it. I'm also using a original Sony 16GB card which is almost full. Is there a step by step guide to how you fixed this problem. Because I'm not trying to mess anything up. Thank you!

 

[duwen]

This is the issue I'm having right now. I don't want to waste space on my new SD card. I only have 32GB on it. I'm also using a original Sony 16GB card which is almost full. Is there a step by step guide to how you fixed this problem. Because I'm not trying to mess anything up. Thank you!

Sorry, I really don't remember the exact process (it was probably around three years ago) - plus I eventually succumbed to having a permanent enso install, so now I run everything from sd2vita and just have 'recovery' software installed on the memcard... it should technically still work the same if I insert a legit gamecard instead of sd2vita, but knowing what a pain it can be to lose/reinstall everything (and risk bricking due to enso) I just switched to larger SD's for an easy life.