So my main reason is this. I want to play GBA pokemon games, which I can play on my actual GBA, but 3DS screen/feel is so much better so Id rather play them there. Id like to after Im done transfer my pokemon to Sun/Moon, which would involve getting the save to a PC and copying them over. Since its an injected game there is no legit way to transfer them... so I need that save.

Is it easy to get the save out? Is it something JK save manager would be able to see?

 

Decrypt9 does a better job. OP, to dump a save with Decrypt9 you just have to run the game you want to dump the save from, save, and then boot Decrypt9. I don't remember exactly where the option is, but it's in there.