1. Put your large game in a seperate folder and Rename the vpk to .zip ( make a backup of original)
2. Now create a new folder and name it whatever you want eg. large files
3. left double click on the newly renamed vpk (.zip file) and winrar will open up and you will see the files of the vpk/zip.
4. Highlight all the files except (sce_module, sce_sys, eboot.bin & icon0.bin) now click "extract to" button and extract all highlighted files to the new folder you created earlier. (you will have to navigate to that folder through winrar's browse menu that pops up)
5. Once extracted, right click those highlighted files (in winrar) and choose "delete files"
6. Now that the files are deleted, close winrar and rename the .zip back to .vpk, now you are left with a vpk which is tiny, eg. 80mb instead of 3gb and all the large files are in the folder you extracted them to.
7. now just ftp the small vpk to your vita and install it, it will create the bubble of the game and it will create the correct install directory in Ux0>Apps for that particular game.
8. Now we go back to ftp and open up that newly created directory of the game eg Ux0> app > (games code) and all that happens now is that you ftp all the contents you extracted earlier into the install directory. and once complete you can then play.
I've installed all the 2gb + games like this on my 4gb memory card.