It does make a difference if you do before or after the main exposure. Either one will work but each produces a different result. Sometimes it is necessary, or you want a certain look/effect, to do both, but it is tricky to get the balance right. A slight pre-flash to "sensitize" the paper, then an exposure/burn in your highlight area on a low filter (doesn't have to be a 00 or 0...sometimes those are too much), then your main exposure on whatever grade you want the rest to be on, then an additional burn, on that filter you used for your main exposure). Balancing all these takes paying attention to what you are doing, and the results you get from them. Trying different combinations and watching those results, will make you a better printer in the long run. Since the combinations are endless, it is important to notice the changes that happen with each combintation.
BTW, post flashing can flatten out the internal contrast of your mid and lower value tones, since it will be putting a flatter exposure on thise subtle highlights, so be careful.

Hope that helps.