Add JKSM.3dsx to your 3ds folder and backup all your saves (look at the help inside, it will tell you what keys to press to do all of them instead of one at a time). Then copy the JKSM folder to somewhere safe. Some games will require you to back up extdata as well.
I googled "JKSM 3ds" and i've found JK's save manager, however currently my emunand does not boot at all (i can still access the homebrew channel)... can i run it from the homebrew/sysnand?
Also, just to be sure:
I currently have a clogged-up 16GB SD with reinand (less than 1GB free), 9.x sysnand, access to the homebrew channel and a 32GB SD i'd like to use.
I'm still unsure about the details of the "move EmuNAND" step (since i don't yet have the new SD and i haven't seen a video of somebody else doing it).
Should i:
A) Use the new 32GB following the guide from step 0 and at the time of moving NANDS i'll load the required software, swap SDs(new->old), save required data somewhere and swap SDs(old->new) again?
B) Use the old 16GB after i find a way to clean it up sufficiently, follow the guide from step 0 and at the time of moving NANDS there will be a way to copy the required data? After which i guess i would copy/paste everything into the new SD (which means the new SD will be essentially a copy)
B1.2) Same as above but skipping soundhax since i can already access the homebrew?
Also: in the guide it's said that "you should follow all instructions from within or applying to SysNAND" (when addressing people with an emunand).
What does this mean? Are there steps where i can choose to perform actions on either sysnand or emunand?
Sorry for all the detailed questions, i'm sure it's not the first time you read them, i'm trying to make sure i don't end up with a brick in my hands.
edit
I've looked further and from what i understand the idea is to "dump" emunand into sysnand and get rid of emunand completely, which makes sense.
I guess my SD will be used to boot and store data (as in, no SD = nothing boots at all), is this correct?
Does this also mean that it's possible that a system update will break the whole thing despite having an extremely early boot?
edit
(luma3ds) "protects the Firm0 and Firm1 partitions of the SysNAND from Nintendo’s Updater, thereby protecting your Arm9LoaderHax installation, and making this hack completely self-sustaining, and in addition, making the need for EmuNAND essentially vanish, as Nintendo’s Updates are no longer any threat to you."
Neat so i guess that isn't an issue. =)