The hidden partition installation formats a part of the micro SD card to act as the NAND meaning EmuNAND will only work on that SD card, cannot be simply copied to other SD cards, but is the least detectable out of the 3 methods. When EmuNAND is installed as a file, it can be moved from SD card to SD card but because of that it is theoretically more detectable than the hidden partition. The internal memory method simply installs EmuNAND into the USER partition of the Switch which Nintendo supposedly does not check which would explain why no one has been banned thus far for using that method. Unlike the other methods, this one is SD card-agnostic meaning its not reliant on the SD card to function since its installed to the internal memory.
And one of the reasons for EmuNAND is a way to separate SysNAND from EmuNAND. If there was any sort of communication between the two, it wouldn't be a true EmuNAND solution which TX's fails to deliver on only just. Regardless of which method you use to install it, EmuNAND still involves modifying the boot1 of your console which shares the same detection as AutoRCM and since no one has been banned for only using AutoRCM, its safe to assume people won't be banned for this slight modification either.
This
thread not only has a link to a tutorial but their Discord server.
If you're not using the hidden partition, you can just clone the 2 SD cards. But that is one of the drawbacks of the partition method; it cannot be used on multiple SD cards without making a new partition on subsequent cards. The upside is that it is less detectable than the file on the SD card which is paranoia at best since there is no evidence Nintendo scans the SD card (the Switch doesn't even check its own USER partition). Speaking of the USER partition, that is where the internal memory EmuNAND is installed which makes it relatively safe until Nintendo adds telemetry for that. And because its installed into the console, its not reliant on SD cards unlike the other 2 methods.