Yeah you need to match the opening pulling the air in to the size opening exhausting the air. If you have a 3' x 6'8" screen door as your input you need to have the vents on your roof at least as big in area or it will create a mini pressure bulb in your house, after the fan. Usually the attic. At that point no more air can get in or out. So when you are hitting the 2/3rds setting is probably when everything has evened out. Just a like a car. Bigger intake and heads, bigger exhaust pipe.
It is advisable to make sure that any floor drains have water in them. A lot of people that have floor drains forget to put water in the trap to keep gases coming back into the house. If you have dry floor drains and a whole home fan, it will suck in sewer gas.