So I didn't really know a lot about Knossos, aside from that it's a combined launcher and installer. So allow me to walk you through my thought process as a completely new user.
When I started to install it and it asked me where to put it I did the intuitive thing I've done with literally every other mod or freespace-related tool I've ever gotten and tried to put it in my Freespace folder, but of course it said don't do that! ...Ook? Well, I guess I'll just put it in Program Files, but that's kind of confusing, why won't it let me keep all my Freespace stuff together? Whatever. So it otherwise installed nicely, but when it finished it said I had no mods! What? I have dozens of them! It know where my Freespace directory is, why isn't it detecting them? So as a test I downloaded BP. Which worked and played fine, but I saw that it had installed it to the Knossos folder. OK, so it keeps mods in Knossos, and retail FS2 in Freespace? Wait, no FS2 is in here too, along with copies of the builds I have. Does it just copy everything? Mods take up a lot of space, can I just move all my old mods into the Knossos folder?
And that's about where I am, now. Don't get me wrong, I'm sure there's great reasons to have all this stuff this way, technically I'm sure it's more rigorous and bug-free or whatever. But, I think some more should be done to explain the structure of how Knossos works, especially if you have a big existing install with a bunch of mods 'the old way' and you want to transition. The old way is comforting and I understand it well, but Knossos has done a bunch of weird things I didn't expect and it didn't explain well, so I get turned off of it.