Apple1 - you can do this. the flue can go through the attic but there are building regulations that govern this. The flue would need to be separated from any combustible material (you dont want a fire!). Also, flues dont like horizontal runs - it can affect the draught. One important thing to have is a insulated flue with twin walls, not a snigle wall flue, insulated flues cost more but have less problems so better in the long run. Your builder would be able to tell you the specifics.