The simple answer: assuming you downloaded the latest version of JKSM, then you need jksm.xml in the same folder as jksm.3dsx. That will let you run JKSM from the Homebrew Launcher without having to use Fredminer to install B9S – but you definitely won't be able to run FBI or install anything in .cia form. (Running JKSM is pretty much the only thing you can do without installing B9S.)
I could have sworn that’s what I did the last time. I guess i’ll look it up again.