Originally, the Check Airspaces was a feature to help you see if you were going to cross any Airspaces to help you plan those altitudes.
In flight, the iFly GPS software will alert you if you are approaching any of those airspaces, just in case you are not paying attention.
The Check Airspaces is a 2D look and does not currently look dynamically at your altitude or your planned altitude. This is something we can put on our Wish-List for future consideration. I hope this helps clear up any confusion. Have a Merry Christmas and a Happy New Year.