Let me start by saying that nothing is worse than having your opponent catch his card on the river, and having to play with 400 chips to face his 1400 chips.
So what should you do in the rare event of you becoming short-stacked?
There are several different approaches to playing with a short stack in heads up poker. Some players like to simply give up and go all in with the next half way decent hand. These are the ones we always hope to be playing when we have the chip lead.
Smart players have patience and don't lose their composure when they have the short stack. Wait for a good hand. If you are short stacked the the point where the blinds are going to knock you out, then you should have already pushed all in. Wait it out for a top ten hand. Try to see the flop without going all in.
If you make it to the flop without going all in, you should either go all in if you hit your hands or count your outs and play accordingly.
There really isn't much to playing a short stack in heads up play. You have to hit your hand and try to double up. It is all about the momentum. If you come back from a short stack, it is a huge momentum shift and you can usually go on to win.