There's not really need for a guide. Each emulator has it's thread with whatever instructions are needed, but it mostly consists of:
*Installing FBI (crucial homebrew to install everything else)
*Strongly suggest you also install FTPD pro, to move files without taking ur SD card out of the console (optional tho)
*Download CIA files into your SD
*Install them with FBI
Try installing 3DS games first as it's easier than emulators, if you succeed go ahead and try with bubble's standalone emulators for genesis, NES and SNES, since those work well and are simple to set up.
If you're ok with that, then move on to DS games, and DS emulators (as in, emulators for other consoles made for DS which can run on 3DS) like gameyob, gbarunner2 and NGPDS. These don't use CIA method so you'll have to research a little bit, but it's easy once you get the hang of it
If you manage to do all that you're good to keep investigating what u want or need on your own i'd say, like N64, PS1, retroarch, and other useful homebrew