Ok. Is he really flat, or just a bit? LOTS of babies get a bit of a flat spot - essentially b/cos they all sleep on their backs now, for very good reason. Their skulls esp in first 6 months are really soft and the constant pressure just makes them flatten.
If it's only a little flat - don't worry! As the head grows, the flat bit will look less, plus hair covers it - if you feel a few adult skulls you'll soon discovere how wierd all out head shapes are ... or so my mate who's a physio tells me
Also, fyi, most babies hit their 'flatest' period at around 6 months, it's probably as bad as it's going to get. But you might want to be aware that it may not go away all together.
Also, it is essentially a very benign condition. There are a couple of studies that suggest some MINOR corelation with other problems, but they are very very slight. So it is, as I undersatnd it, essentially cosmetic.
If it's bothering you, you might want to try some repositioning, but it gets harder after 6 months as babies tend to wiggle about more. There are more invasive therapies availble, but I ain't even going to tell you about those unless you reckon you're really worried ...!! (my dd is currently having more invasive therapy ... still not sure if it's worth it/completely pointless!!)