I tried that back in pre-release, and it didn't do what I expected. It was still opening the 32-bit binary regardless of the options written in. If that works now, that's great, although I just changed my command-line options to be just KSP.exe and it still opened the 64-bit binary. It seems CKAN is now defaulting to the 64-bit executable. Regardless, as @Holyvision said, if the game is opening in 32-bit and that's not what you want, and none of these suggestions works for you, you can always run KSP through Steam or the actual executable in the game folder.
Edit: It appears I might be wrong. My CKAN has an option that I'm using to run the game through Steam, which is apparently using the Steam default. @Plague006 may be entirely right in this regard. I will stand by the last part, as obviously Steam is defaulting to 64-bit, at least on my machine, and it gives you the option to play in 32- or 64-bit, so you can always start the game from there if the CKAN option doesn't work for you.