In theory, I think it makes a difference. Scrubbers are at the end of the chain where the air is finally gone. The reason you have a scrubber is for the air to pass through the carbon and deodorizing it from there.

Pics would help a lot. I am visualizing a scrubbers like this one Cannabis.com Forums Message Boards - Medical Marijuana, Cannabis Club, Dispensary, News

But I have a sneaky suspicion its not at all like it if the fan is on the end????