Disclaimer: The following is not standard or approved...
I would run a 3 to 4 inch pipe down the chimney and connect it to the blower intake so that the intake air is at the same pressure as the exhaust regardless of the wind.
You would have to have two U bend pieces at the top of the chimney so that it draws in fresh air and not exhaust.
This plan would also have the advantage of pre-heating the incoming air and thus increasing efficiency.
Running the air-intake separately would be a more standard method. As long as the air intake is near the chimney exhaust the pressures would be about the same.