My good sir,
I haven't really attempted to deal with the steam installation, I shall attempt to guess.
I do reckon you need to direct knossos to wherever freespace 2 is installed.
From the settings section of knossos, expand the 'knossos' section and then click 'browse' to set the 'data path' and point it to the freespace 2 installation in steam.
The path is probably something along the lines of "C:\Program Files (x86)\Steam\steamapps\common\Freespace 2" for windows.
You can dump your currently downloaded mods into that steam freespace 2 installation directory, and I think knossos will pick up on them. Or you can just redownload them to be safe. I'm pretty sure knossos doesn't actually keep any metadata though, so most likely if you just move the mod folders it will work.