Could you please explain what you mean? I'm not sure I understand what the purpose of everything I did is, and formatting made it more confusing.
What I mean is what's the point of doing all of the emuNAND stuff?
Why shouldn't I just downgrade and install RxTools directly?
tl;dr basically it just makes playing games easier and keeps your sysNAND safer so it doesn't get bricked and you still have a working system
Since I can only relay what I've read about it, bear with me, since I'm still kinda new to this stuff as well.
emuNAND = emulated NAND. You know how you can use savestates in emulators for games and, if something doesn't go the way it should or you die and you want to keep all that progress you made without restarting, you just load the savestate? It's a sort of safety net that keeps it so you can continue using homebrew. Accidentally updated in emuNAND? No problem, so long as the NANDs are unlinked. Bricked your emuNAND somehow? No worries, just install a backup. Want to play games on the latest firmware without hassle, but still want to keep your system hacked? Just update emuNAND and keep your sysNAND where it is. Think of emuNAND as a safe playground for homebrew. If something goes wrong with your sysNAND, you're in trouble. But with emuNAND, it's no trouble. Your console still works and you can just redo everything.
So what happens when emuNAND is created and the NANDs are linked?
When you create an emuNAND the SD card gets formatted, and a separate partition is created specifically for the emuNAND. Where does the information for that newly created emuNAND come from? sysNAND! Your emuNAND, right after creation, is an exact copy of your what your sysNAND was. From that point on, certain things that you do in sysNAND are mirrored to your emuNAND.
At this point, I'm not sure if certain things you do in emuNAND are mirrored to sysNAND, so for all intents and purposes, let's assume it works both ways. Biggest thing is this: if your NANDs are linked, and you update one of them, the other one gets updated as well. For the New 3DS, emuNAND is only going to work up to
9.5. For the Old 3DS, it's 10.3 (the latest as of typing). Thing is, you want your sysNAND to stay on an exploitable version with kernel access (9.2 works well for this as it also gives us the possibility to 'cold boot' into emuNAND). So if you update one by accident, while linked, the other one is also updated and you have either an unusable or unreachable emuNAND.
Ok, great, but how do I keep them separate and
unlink them?
In order to unlink the NANDs, you format one of them. Think of it as just doing a system format and starting fresh from there - new friendcode, new NNID, the works. Once formatted, they are no longer linked in the ways mentioned in the previous paragraph. Once unlinked, you can safely update emuNAND without having anything happen to the sysNAND. Thus, exploits and kernel access remains in sysNAND, and your emuNAND is updated so you can play games that require you to be either on 10.3 or have eShop access to update the games themselves. For us New 3DS users there are ways to do these things unofficially, but I'm not going to explain that here.
Lastly: "
Why shouldn't I just downgrade and install RxTools directly?"
rxTools allows you to do some neat stuff, namely installation of any .cia without having to worry about signature checks. Yes, rxTools can be run alongside sysNAND to function as it does in emuNAND, but because of what it allows you to do, you have the possibility of bricking your sysNAND. And you can't recover from that unless you have a backup
and it's hardmodded to allow NAND injection. Besides this, games that require a firmware higher than 9.2 to run won't unless you do some 'magic' to them if you plan to stay on 9.2 in sysNAND. It's less of a hassle to play games, really, if you're using an updated system, no?
Apologies for the text wall, but I wanted to go sort of in-depth about it.