You can add / delete instllations of KSP through File -> Select KSP Install. Theoretically you can manage several KSP installs with CKAN.

Or from a command line, ckan.exe ksp (list|remove|add)

The only problem is that whenever I open CKAN, it says 'ERROR: Cannot locate KSP in C:/etc/Program files/Steam/KSP and just instantly crashes. I have this problem with any version of CKAN I install, but I will try the command prompt suggestion.

Can't get even the command prompt to work... I don't know what to do now.

halp

Does it crash when you run this?

ckan.exe ksp list

If so, you'll need to get into Registry Editor, and go to HKEY_Current_User/Software/ckan to clear out your data there.

Wait, do I do that in the command prompt that opens with CKAN, or open an entirely different one?

Not sure if this will help, but hopefully someone can debug it and figure it out for me.

 Unhandled exception:
 System.IO.FileNotFoundException: Error reading the c:/program files 
 (x86)/steam/SteamApps/common/Kerbal Space Program/CKAN/downloads directory.
    at System.IO.FileSystemWatcher.StartRaisingEvents()
    at CKAN.NetFileCache..ctor(String _cachePath)
    at CKAN.KSP..ctor(String gameDir, IUser user)
    at CKAN.KSPManager.LoadInstancesFromRegistry()
    at CKAN.Main..ctor(String[] cmdlineArgs, GUIUser user, Boolean showConsole)
    at CKAN.GUI.Main_(String[] args, Boolean showConsole)
    at CKAN.CmdLine.MainClass.Gui(GuiOptions options, String[] args)
    at CKAN.CmdLine.MainClass.Main(String[] args) 

My current KSP directory is C:\Games\Steam\steamapps\common\Kerbal Space Program by the way.

Okay, I've fixed the issue. Hooray for unlocker software!
Turns out the issue was that the CKAN directory had been locked for no reason when I uninstalled steam... thanks windows.
I deleted the file via an unlocker tool created a new dummy CKAN folder, and voilà! problem solved.

Thanks everyone who tried to help, I just did a bit of digging around in files and figured it out.

@politas Thanks so much! I hadn't played in a while and Steam auto-updated. Tried everything to get CKAN working. The regedit worked!~

A bit late, but my CKAN launcher, when asking for my install path (I changed it), the installer itself won't let me select it properly. It'll show the install menu, but instead of having a selecting a button, it only has a "open" button, which pretty much does what you think it does. I cannot therefore select my install directory for KSP and play the game. I feel like it's something really simple I'm just missing, but can't figure out. Please help.

@D4rKing, select the buildID64.txt file.

I owe you my life. Thanks!