Mod Organizer found both Skyrim and Skyrim launcher fine. MO has a Mod Organizer folder which is sitting in the Skyrim directory next to the tesv.exe. BOSS when I installed it did not make a folder, but threw all its stuff loose in the Skyrim directory. (That is, my skyrim directory, the one with tesv.exe in it, has "boss gui.exe" as well as boss.exe and bosslog.html, and boss's uninstall executable. I am not sure why MO didn't find BOSS, but even after I added BOSS GUI manually to MO and it can now be launched from MO, it says skyrim is "not detected" like it does for the other games.
Update: I just now accidentally clicked BOSS (regular, not gui) in my start menu looking for MO and ran it that way. Now when I run BOSS through MO it can find skyrim. It got identical results run both ways, but that is probably expected in this specific case since I currently have no mods installed and have all the DLC deselected both in the skyrim launcher and in MO.
It would appear that there is something BOSS is looking for to see what games are installed that it cannot find from within the virtual file system, but also that when it does find it it writes something to somewhere it can read from within the virtual file system. Not knowing how BOSS decides what it can detect, I do not know for sure if this is correct, but it would explain my observation (and if anyone has more details on this, I would probably find it a fun read).
I may end up starting over if I can't find why there are loose folders named after other games in my skyrim directory. I bet they were added by either MO WB or BOSS but I do not know which. If it helps, the folders are called "Fallout 3" "Fallout New Vegas" "Nehrim" and "Oblivion" and each has a folder ".git" inside. But then so does the skyrim/skyrim directory (ie, inside the skyrim folder that has tesv.exe, there is a skyrim folder which contains the .git folder) but it also has a BOSSlog.html masterlist.txt modlist.old SkyrimPrefs.ini and userlist.txt. I am suspecting these are BOSS folders. Should I delete the ones that are not for skyrim? Or did I do the installation wrong?
I'm currently thinking I should read the whole guide two or three times before next attempt and take notes to look for anything else that might catch me by surprise. Once I've got an install of STEP:Core, I may have some suggestions for guide clarity. (I'll try to find the right thread for them.)