You definitely want to buy the wheelset before you get the brakes. Then you just measure the needed brake reach and get brakes that have a range that encompasses the reach you need.

Brake reach varies from brake to brake. The longest I know of is the Tektro R556. I use it on the front of my main fixed gear and it works pretty good. But if you can get by with shorter brakes, you'll have many options. Ask the roadie forum for a brake recommendation since many more of those guys actually use brakes on their bikes.