Powersaves is the best option for backing up and restoring saves in the same cartridge, but there's no choice in software, you have to use yours, and likely the cable that comes with it will suck. So, get a (longer) one. Also, Powersaves files are encrypted, you have to decrypt in order to edit on PKHex, but even then, you can't write it back into the cartridge. Only Gateway ROMs with SaveDataFiler support that. I don't know about Cybersaves in regards to multiple cartridges and saves, but I do know that's the most complete way to backup, restore, and edit in PKHex. The catch there, only Japanese 3DS and games. The only other ways would be through Gateway ROMs, or Ram2sav. The latter can handle saves in multiple cartridges, but you need a 3DS not running 9.5.23+. Also, ramsaves are partial data, things that are constantly updated, like game time, can't be edited. Party pokemon and trainer info also can't be edited, but the stuff typically edited, can be. Namely, pokemon, items, moves, that stuff. Plus ram2sav's a browser exploit, and free, so it's relatively quicker in its usage.
I go with ram2sav the most, but sooner or later I'll invest in the Japanese way.