Yes I did this other day, you can't select it manually, but you can set it as the directory using the terminal. Press ctrl + alt + t to bring up a terminal window and type (may need to CD to wherever your ckan.exe directory is first) mono ckan.exe ksp add default /path/to/your/install followed by mono ckan.exe ksp default default With regards to your question about install directory, well in linux files are grouped by function rather than what program uses them. So for example some executable files might be installed to /usr/bin, some required libraries (which could be shared by different programs) could be installed to /usr/lib, other files in /usr/share and so on and so forth. Steam is a bit of a funky one in that it apparently installs to the home partition (which is for user documents / music / pictures / videos / etc). Not sure why.
