Theoretically, yes, you should work backwards and build a 6" diameter system.
However, you first need to evaluate your intended use and needs and decide if a 6" system will be big
enough to give the heat you need. It would be cheaper to build what you need now even if it means replacing existing chimney pipe, rather than having to scramble to rework, replace or supplement something that turns out to be too small.
So what is your climate, building characteristics and desired heating use?