I'm not sure, but using amiibo emulation and overclocking may put you at risk of getting your console banned. Overclocking should be alright for offline games, but I'm not familiar with it. You can check
here on how to avoid getting banned.
This thread has some additional info as well.
Personally, I'd keep the sysNAND clean and use it only for legit games, without any modifications to it, and keep all the CFW stuff, running homebrew apps and playing backup games on the emuNAND while blocking Nintendo servers at the same time.
sysNAND and emuNAND partitions are hidden so that users don't mess them up by accident. The only partition you see when you is the microSD card partition which is shared between them. Homebrew apps usually go inside
switch
folder, If you use Homebrew App Store app to download new homebrew apps, they're installed into the correct directory automatically. Note that going online on a hacked console is only safe if you have blocked Nintendo servers by using
DNS MITM.