Hello.
I believe the easiest way, as far ad dumping games goes is using an app to dump the installed game as an NSP and carry it over to your emuNAND by installing it with title managers.
for saves you could use Checkpoint to back up the save on system NAND and use it on emuNAND thereafter.
But this is risky and will result in a ban, so as far as I know, there's no "legit" way of carrying your stuff from sysNAND across emuNAND without the ban risks associated with it. and there's nothing to mitigate that risk either. So at best, for now only NSPs are your option.
Altering the Nintendo folder is highly recommend to stay away from. it will render your games, both on emuNAND and sysNAND unplayable so messing with it isn't worth your time.