Also protect your frame latching mechanism. If you don't have the plastic cover that came with the bike, you can improvise and use a tennis ball, crumpled newspaper, etc. Use your imagination.
Now dump the frame into the case.
Next goes the rear wheel with the cassette facing the frame. The front wheel then goes on the outside. Stem and seatpost then goes on top of the frame.
Put your wheel quick releases and pedal in a bag and secure to the frame. With the new post 9/11 airline security rules, we suggest securing the frame, wheels, seatpost and bars together with bungee cords. We also suggest protecting the folding stem pivot (tennis ball with a slit, crumpled paper etc.)
Unfold all the flaps to protect the bike at all sides.
That's it !. You've got your bike packed and protected even in a softcase.