In the past all I've done is use Hekate to get to edizon and edit my savefiles, nothing more. So my goal is pretty much to just use emummc to do that from now on instead of just using my sysnand for it. But since emummc and sysnand are somewhat separate what I was wondering if any saves file I edit on emmunc can be transferred to sysnand.
Yes, they can, with Checkpoint but that would involve booting CFW on sysMMC to restore the save... This defeating the safety you're trying to achieve with emuMMC
If you boot CFW on sysMMC you are running the risk of a ban. The risk for save editing single-player offline games seems relatively safe, it's no guarantee... And it doesn't help that no one has been getting banned recently so we don't really know what Nintendy is up to.
The safest way is the make emuMMC and play the games you want to modify there and leave sysMMC alone.
If you're going to boot CFW to recover modified saves from emuMMC then you are wasting your time for the same exact risk and might as well just keep modifying saves on sysMMC.
It's best to not touch sysMMC with CFW at all.