Try not to worry about it!
Your boobs are never 'empty' - they can get full in the early days but even when they feel like they're completely empty your body will continue making milk on demand (even if you can't express anything, baby will be able to get some directly). So the flow may be slower when you feel empty but your baby will still be getting milk. As long as he is still having a normal number of wet and dirty nappies and he's otherwise happy and healthy, he is fine.
What he is doing now is boosting your supply to meet his growing needs. When he drinks the pre-made milk and continues to feed after that, it lets your body know to make more for the next feed. Over a few days or a few weeks, your body will catch up to his needs. It's cluster feeding and it's totally normal... not only normal but great! It's your baby and your body working together to get what he needs. The best thing you can do it continue to feed on demand. If that means 3-4 hours in the evening (the most common time for it), get yourself a couple of DVDs, some chocolate and a nice drink and try to enjoy the time. It doesn't last long in the grand scale of things.