The key with the large head and very odd carrying case is considered to be the main key, I believe, while the single, thin blade key is the spare. I've no idea why they made such a fancy key/case combo - probably from the same brilliant Japanese engineering mind that put the f'king fugly brown paint on several parts and thought it looked great enough to remain on every Gen II sold through current...regardless of skins color. (IMO, hasn't looked good with any of the skins color so far.) And quite probably the same little dude that thought it a good idea to mail out non-matching #'s for the frame badges to original 2009 buyers -aggravating little chitt.
They only come with the one large key/case, and the other thin one. No bike I know of came with two of the large odd keys.