Phew, so I installed rxtools following
this guide, installed the legit cias (I can't remember if I installed them to sysnand or emunand, and I still don't know which one I should have chosen), and then did the mset thing so emunand could be loaded from the settings menu. Everything seemed to be running fine. The legit cias wouldn't start in sysnand but updated and loaded fine in emunand, so I showed my nephew how to get into emunand and then left him on his merry way. He told me later that the mset trick stopped working so I told him to go to the browser and that loaded rxtools so he could choose emunand. But now he's telling me that all of the games have disappeared except one.
I guess what I'm asking is should I have installed those cias to sysnand or emunand, and is that why they have disappeared from both the sysnand and emunand menus?