It's pretty simple, luckily. I'm actually planning on doing this, can you link me the one you found?
So, boot into GM9. Navigate to whichever NAND you're changing's CTRNAND (1: for SysNand, 4: for EmuNand), then inside navigate to the rw folder, then to Sys, then you'll have the 4 files. Copy the LFCSB to GM9OUT, and store it in a safe place. Take the public one (be careful not to mix them up) and put it where is was. Now, go to your SecureInfo_A (same dir as the LFCSB), open it in the hexeditor, and look at the last 3 lines. You'll see your serial. Change that to something a bit different, but REMEMBER YOUR ORIGINAL! Then you're good! If the public gets banned, change your serial back to it's original form.
Do not worry, if you're on an old firmware, it'll bug you and bug you, but it will not auto update. This is not Wii U.
Yes, you can use DSIWareHax. If you have a hacked 3DS already, I highly recommend it, as it can be done for free. (Single system version is difficult & not free).
Yes, 11.6 is the current firmware. Take a look at
the first page of the thread, it may have a few questions answered.