So, if you install a cia file, can these be played without using the gateway 3ds?
Sorry for all the questions, I'm new to this.
.3ds files act like game cartridges. Gateway saves their saves to the sd card as <titleid>.sav.
.cia files are like installers for on-NAND games. I
think their saves get saved to NAND, but I'm not sure.
SaveDataFiler can extract and inject saves for at least .cia games. I'm not sure if it works for .3ds games.
There's also Save Data Transfer Tool from eShop, which can transfer from cartridge to NAND.
You need to have the Gateway card inserted when you start "Gateway mode". In this mode, you can play the games on the Gateway card, as well as games installed to NAND. I don't think you need the Gateway inserted to start a game installed on NAND, as long as you are in Gateway mode.
You also need the Gateway card inserted to start "Classic mode", which is used to play retail games without requiring an update and with region-free. In order to avoid updates, you need to install Emunand, which is a copy of the system nand. It gets loaded from your SD card. You can update it when Gateway says it's safe.
That's just an overview. It's also only how things
used to work, not necessarily how they will continue to work when the update comes out.