Is it possible to have another instance of the game?

[sirOrange17]

Say I wanted one version with lots of mods than another version with not a lot, how would I have to separate game versions. Would CKAN work with this? 

[DeadJohn]

Yes, you can have multiple folders with different version of KSP, different mods, etc. CKAN works fine. Specifics depend on operating system and how you bought the game.

Just take whatever folder you currently use for KSP and make an entire copy of it with a new folder name. You now have 2 completely independent copies of KSP. You can point CKAN to one folder at a time to manage one copy's mods.