Unless you are trying some complex unsupported setups to play around with you should do nothing in sysnand. The main purpose of emunand is to make sysnand dead to you. Bottom line if you don't want to use emunand exclusively (classic and gateway mode) then you are jumping into a into a snake pit. Plan on spending more time reading threads and expirmenting than actually playing games.
I understand how this is all a little confusing. Understand as well that Gateway is not perfect especially when it comes to saves and encryption. It will what you say you want it to do and only gets complex if you try to make it comples by stretching its capabilities.
I get what you mean.
I'm just wondering what kind of steps are needed to be done to be able to still use the stuff that I already own, as well as what Gateway and emuNAND and whatnot, can offer as well, without screwing either of the two up.
And that's the issue I keep seeing with these guides. They only look at one extreme, which is just emuNAND by itself and that's it, more or less having no care in the world if you end up screwing your whole 3DS up as long as the almighty emuNAND works.