if its a n3ds you can still use browserhax (for now?) or cubic ninja/smashbros* (or a sky3ds flashcard with cubic ninja/smashbros* 3ds rom) if you have a o3ds you need cubic ninja/smashbros* (or a sky3ds flashcard with cubic ninja/smashbros* 3ds rom)
also if you have ocarina of time and temporary access to homebrew channel (or another 3ds with hbc access) you can set otthax up on the game card then use it for homebrew in your own 3ds
*smash bros hax requires a more complex setup on your end*
i tend to say this often but that's an old setup now those of us still in the loop are using rxtools
[Tutorial] Installing rxTools Custom Firmware - (3DS and 2DS) (the creator of pasta would even tell you to use rxtools as they are now the same project) updating sysnand to 9.0/9.2 in order to use themehax (in the link) to autoboot cfw when the system is powered on
https://m.youtube.com/watch?feature=youtu.be&v=LcAMVMpXjzo
and as far as an answer to your save issue
You can use either one of the these: Savedatafiler (use 3dsdb.com to find title IDs and Serial codes), NTRCFW 3.0 + Save plugin (You hold L while launching a game to make a backup; don't have to look up title ids to use this!), or the homebrew save managers like TDVS and SVDT (these are easy to use too BUT the compatibility with some games are not perfect).