Do it once then keep your console in sleep mode instead of turning it fully off.
You can boot normally into the original firmware (sysNAND) and use purchased games. This is a step in updating the official firmware so you can copy it to the custom section.
To run, ahem… backups, yes you need to inject a payload to turn on the switch. Unless you have a mod chip that does this for you. The custom firmware lives in a section of your SD card that is a copy of the internal memory (emuNAND), which Nintendo can’t detect if you boot into the official mode.
To avoid a ban, IIRC you must not use the custom firmware *online*.