Just attach it to the carseat, if the carseat doesn't count then niether should the base. I would call the airline to make sure. I recently flew JetBlue, and they allow you to take one specialty item per passenger, so for me the carseats were that item. Just call and yoou can ask them (whichever airline your going to use) any questions you need to know. :)
If you're taking the carseat on the plane (I assume you bought a seat and are using it) wouldn't you need the base to buckle in the seat? If you don't, and you're checking it, I'm 99% sure you don't have to pay for it, because you don't pay for checked carseats.