I'm assuming you're looking at a piston port engine. If that is true the fuel/air mixture is sucked into the crankcase under the piston (not on top) where you may be looking. Then upon the down stroke of the piston that fuel/air mixture is pushed up out of the crankcase through transfer ports on each side of the cylinder and onto the top of the piston.

My mechanical engineering son would try to explain this to me forever but I have to see a picture.

http://www.animatedengines.com/twostroke.shtml

The little movie link above shows a 2-cycle engine to illustrate the principle but it is confusing as well. Don't get me wrong here...thanks for the movie link. It shows an intake valve that doesn't exist (except for reed valves) and it doesn't describe or show transfer ports well. It also doesn't show how a piston port engine works. Piston port engines use the piston as a valve instead of having a reed valve or rotary valve.