Yes, more info would be nice. Some of this is different from what I have read before.
So ejecting the SD card lets me keep the emunand partition, yes? What happens to the system itself (firmware, settings, etc.), and what will happen when the SD card is placed back afterwards? There is no need to backup the SD card?
Ok, so how the 3ds works, is when you purchase a game it installs shortcuts to the home menu, on the sysNAND, and routes them to the game on the SD card. The issue when you format, is that it deletes to shortcuts, with no way for you to re add them without re downloading. So if you pop an sd card, thsts why you don't get the games.
So when you copy your files to your SD after formatting, it will never recognize, and your data will be lost. If you keep your SD in, it will also be formatted, therfore destroying your emuNAND. So what would be the point? You will be back at square one with no emuNAND.
Question 2: So ejecting the SD card lets me keep the emunand partition, yes? What happens to the system itself (firmware, settings, etc.), and what will happen when the SD card is placed back afterwards? There is no need to backup the SD card?
When you made your emuNAND, it made a 1:1 copy of your sysNAND. After this, they are now separate entities. Altering one, will not alter the other. That's why if you create a folder in emuNAND, it won't be present in sysNAND. When you format one of the two, it will not format the other. That's why you can update emunand without updating sysNAND.
when you place it in once again, it will only display what it has a shortcut of. So it will essentially won't share any of the games or w/e. If you want to access the stuff, you must go to emuNAND.
When you format, you do need an internet connection, but don't worry, they won't update your console. it scares everyone, but just rest assured, you will remain on 9.2 or w/e fw you were on.
Darn, I should write a tut for this stuff or sth.