Eshop/NNID?
While you can entirely bypass the eshop by manually getting things like game update cias via warez sites, many people prefer the convenience of eshop access (and, of course, the ability to legally obtain games). If you're using an o3DS (or using ReiNAND on a n3DS) you can update your EmuNAND to the latest firmware! If you do so, you'll now have access to a fully exploited AND fully updated system when EmuNAND is loaded!
As for NNID, you should only set up your NNID on either the SysNAND or the EmuNAND, but not both. When you setup your NNID, it becomes permanently associated with your 3DS hardware (you need to call Nintendo to attempt to undo this). Fortunately, you can relogin to NNID as many times as you want on the same hardware without calling Nintendo, even if it's on different firmwares/NANDS. Since you're not going to be able to access the eShop from SysNAND in most configurations anyway, I recommend setting up NNID in the EmuNAND.
If you previously configured NNID on your console and set up your EmuNAND without removing it first, your NNID is attached to both EmuNAND and SysNAND simultaneously and may cause problems using the eShop or online features. To undo this you'll need to use "Other Settings" -> "Format System Memory" under the Settings app in BOTH EmuNAND and SysNAND to fix it. This will erase your games and save data on both NANDs. The only way to get your games again after formatting is to redownload them via the eShop or warez sites. You can preserve your saves by using svdt to export your save before formatting and then reimporting it after formatting, so make sure to export any saves you plan to keep before formatting!
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Vetusomaru:
psychic academy. lol. it was meh even back then when i bought volume 1. also same author also made one of the manga adaptions of Escaflowne.