TegraRcmGUI is a Windows program that injects a payload to a connected Switch booted in RCM mode, so that it can load your custom firmware instead of just the official one. There are
alternatives to TegraRcmGUI for Linux, Mac OS, Android and Chromebook devices. Another alternative is to install a modchip on your Switch which will inject a selected payload for you. Except for the modchips, all these options are free, so you can choose which device you want to tether your Switch to when injecting a payload.
You only need to do this when you power up your Switch. If you just put it in sleep mode instead of shutting it down, and don't let the battery deplete completely, you'll never need to inject a payload more than once.
To back up your NAND, you can use
Hekate. It can dump your NAND to your SD card and restore from a backup as well as doing some other things. Hekate comes in two parts, the actual software that you copy to your SD card and the payload that you inject from one of the options above (currently, the latest payload is "hekate_ctcaer_5.7.0.bin").
To actually use the hacked Switch, you need to install
Atmosphère to your SD card and inject the "fusee.bin" payload that comes with it. There are two ways to do this: Either with TegraRcmGUI (or one of the alternatives listed above), or from within Hekate.
I hope I've answered your questions.