The rocket Launcher folder can have implications by placing them all together. As RocketLauncher is now stand alone it also makes sense to keep em sep. This becomes more apparent after you start configuring more and also gives you more options hassle free in the future.
Another good idea is to have the emulators in root to keep those free of clutter. So if I was to make another build I normally keep it to...
HyperSpin
RocketLauncher
Emulators
Roms
All as my root folder structure. But again its all personal taste. The main thing to remember is RL out of HS folder. Don not use anything numerical on the Folder names. But its all up to you how you sort it.
As for choosing guide.. all depends if you like to do things visually or verbal... they all get there in the end