I’m just wondering if there is a way to Transfer my citra save game to my digital 3ds version of my game?
It sure is. The easiest way is to have JKSM installed on your 3DS.
First you should use JKSM make a backup of your saved game on the 3DS, which will create the right folders you need on your SD card. Put the SD card in your PC and browse to that folder. It will probably be something like SD://JKSM/Saves/ (game name) / (what you named the backup) /
And there should be at least one file in there, maybe more, which is your saved game data.
On the Citra menu, right-click a game and select “Open Save Data Location” and it’ll take you to a folder in your Citra user data that should have the same file(s).
Copy those files from the Citra folder to the one on your SD card, put it back in the 3DS, and use JKSM to restore that saved game data to the digital game on your 3DS.
We generally recommend Checkpoint over JKSM since users have reported having a lot more issues with JKSM than with Checkpoint.