By default (if you checked absolutely nothing) turning on your unit would boot straight to emuNAND. [which if you're using updatedsysNAND you wouldn't have = black screen]
By checking updated sysNAND, the system now auto-boots to sysNAND instead of emuNAND if you touch nothing. [with firm0/firm1 patches applied]
If on updated sysNAND you for some reason wanted a emuNAND, holding L when it's chekced means it'll boot emuNAND with 9.0 firm (e.g. you wanted to use gateway))
Holding R would boot whatever firm (mostly 10.4 at this point), and if you had dual emuNANDS, holding B with R would boot the second emuNAND.
For someone who's just using sysNAND only, just check updated sysNAND/Use Pre-patched firms and be done with it.
As to reiterate the top, if you didn't check UpdatedSysNAND and tried to boot, it would just boot your emuNAND. If you didn't have an emuNAND, it would either error out, or just hang on a black screen.
Actually here's a better line straight from the thread about what happens when nothing is checked:
Regular mode:
- Normally emuNAND is autobooted. Holding B boots the second emuNAND (if present). This has no effect if you only have one emuNAND.
- If you hold R on boot, sysNAND will be booted with the firmware.bin on the SD card.
- You can boot SysNAND with the 9.0 FIRM. To do this hold L on boot. If you're not using A9LH and your console (O3DS) is not on 9.x, it will be detected and it will output an error.