The advantages are that, once it's set up, you have a 100% boot rate (I don't know, has menuhax fixed this? Last I used it it worked about 9/10 of the time), a much faster boot (maybe a second longer than usual), no need for EmuNAND at all (hello free SD-card space!), brick protection (ability to create/restore NAND updates before the system even fully boots, saving you from anything but a GW brick) and some tentative protection against future system updates (because it sits in the bootloader and protects itself from being overwritten, unless Nintendo gets creative in getting rid of it). Setting it up is a bit of a hassle, but in my opinion, totally worth the effort.
In your case, a good idea might be to back up both your NANDs, format SysNAND using TinyFormat, THEN follow the whole guide. Then, after you're done with *everything* else, restore your EmuNAND to SysNAND, using Decrypt9 to keep a9lh. That way, you'd have all your CIAs installed just as they are now, with an updated 11.0 SysNAND that you can boot straight into from a9lh with luma/etc.
