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3DS VC Pokemon Save Transfer Guide

This guide is about the 3DS Virtual Console versions of the Pokemon games and how to move the save files around to different systems.
In my case, I did this so I could play the same Pokemon Red and Blue saves on 3DS, the emulator mGBA, and more importantly on my cheap flash cart.
In particular, I am frustrated that the VC versions of the games have extra functionality, but are strictly as if they were played on a Game Boy and don't have the extra color that you would find on a Game Boy Color.
The GBC, unlike the Super Game Boy, didn't add a lot of color to Red and Blue, but did make it so the game had essentially one extra color.
I already had the flash cart that would allow me to play this on real hardware, so I figured why not play the game as I want on my GBA SP and move the save back to the 3DS when I wanted the trade capabilities with other 3DS users.
Theoretically, if you had a Super Game Boy with a flash cart or a cart flasher to play this on Stadium 2 via the Transfer Pak then you should also be able to use this same method to play your 3DS VC save on a TV, but at the time of writing this I don't have a Super Game Boy (1 or 2) or a cart flasher to try that.

This guide is for those that have already modded their 3DS. If you have a non-modded 3DS, this guide will be of no help until you follow the guide at 3ds.hacks.guide
And for those that do have a modded 3DS with CFW, make sure you have Checkpoint and if you're doing this on a New3DS then I would recommend using FTPD and a compatible FTP program on your PC to move the files around so you don't have to take the MicroSD card out repeatedly.
It makes the whole process much smoother. For Windows, I would recommend Filezilla since it's what I've used for the last decade for most FTP things, but source your own if you feel comfortable enough to do that.

So to start, make sure you have a save file already on your 3DS VC copy.
Of course it would reason that you can't tranfer a save that doesn't exist, but even if you're intending to transfer a save to 3DS it's still important because if you don't have a save then the game shouldn't appear in Checkpoint for you to add the save to.
So either way, make sure you've saved the game and can find it in Checkpoint.
Make a backup of your current save, feel free to make however many you want, but I would recommend making one named something identifiable that you can use as your backup to send out or receive saves with.
In my case, let's use SEND OUT and SEND IN, respectively, but this isn't required.