So when I plug it in and open that .jar I presume I need to open the v3 .sav and then save it? To just simply back up all the sav files?
LSDJ Manager will not pull the .sav file off of a cart, that's what transfer software is for. LSDJ manager will just help you organize your .sav files better.
Example: Say you have a few carts with a bunch of works in progress and 1 or 2 complete songs. You back up the files using your transfer software to get the .sav from your cart to your computer. You load up LSDJ Manager and open up the .sav files you now have on your computer and save the song files individually. Now you have a bunch of individual song files and you can throw all your complete songs into a new .sav file and put that back onto your cart using your transfer software.