For both 3DS and DS mode flashcarts you can extract saves the same way you do with legitimate cartridges. Not sure if you can just edit files on DS flashcarts since they would be in the microSD in the card, worth googling (maybe someone else will answer that)
You don't need a flashcart, unless you were already playing the game on one. Use JKSM to extract the saves. It comes as both 3dsx (for plain homebrew) and cia (for CFW). If you're playing the game on a flashcart make sure it is showing on the cartridge icon, and you might need to rename the sav file to get JKSM to recognise it (look at https://gbatemp.net/threads/importing-gateway-saves-to-cia-games.425743). If it is on a real game cartridge then just have the game inserted when you open JKSM, don't need to rename anything.So I could extract the saves from any game (like Pokémon Omega Ruby) using the flashcart and put them onto my microSD to at least TRY and edit the saves? I do have an SD adapter where it's like a regular sized SD card but reads micros by inserting them in it. Also I'm using a 3DS, not sure if that helps.
You don't need a flashcart, unless you were already playing the game on one. Use JKSM to extract the saves. It comes as both 3dsx (for plain homebrew) and cia (for CFW). If you're playing the game on a flashcart make sure it is showing on the cartridge icon, and you might need to rename the sav file to get JKSM to recognise it (look at https://gbatemp.net/threads/importing-gateway-saves-to-cia-games.425743). If it is on a real game cartridge then just have the game inserted when you open JKSM, don't need to rename anything.
In that case you can't edit your save data, sorry. You're more likely to be banned playing with a 3DS flashcart because if you forget to use a private header and play online, you'll be banned pretty quickly and will have no way to fix it, whereas with CFW it is only a small risk and you can unban yourself in five minutes.Thing is, I don't have homebrew on my 3DS. I used to use it before and it was fun, but since the dark days of May 2017 (aka the ban wave) I've strayed away from the homebrew scene. Thing is if you use homebrew then you're bound to get banned from online play and eshop use, so I feel like a flashcard is my safest bet. Correct me if I'm wrong.
Sky saves to the flashcard's microSD (as any physical game saves the main save, as opposed to extdata, to the card itself)For 3ds I know gateway stored them on the SD not sure about sky3ds