I bought a Kohler Class Six toilet that has a black cylinder in the middle, not a flapper system. How can I tell if I bought the right toilet, is it a 10" rough-in or a 12" rough-in? The condo that I live in was built in early 2006, so I assuming I bought the right toilet for a 12" rough-in. When I take the tapemeasurer from above the baseboard to the bolts on the toilet, it measures 11 inches.

If the center of the closet flange is 11" of the wall you will probably need a 10" rough toilet. The year a building was put up does not really have any effect on the toilet rough in. There was probably a floor tress or other structural member set in the way of putting the flange in the correct spot for a 12" rough.
Your new toilet should say on the box if it is a 10 or 12" rough.