Can anyone tell me how Wrtightsoft treat a a insulated roof deck compared to a insulated flat attic.

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The best way to determine what RSU does with scenarios like this is to do it both ways, then compare the reports to each other. The "component constructions" report (found in the Load section) will show you the gains losses attributed to each portion of your building. You could compare the two to each other here.

The general difference is that different roof types in RSU reference different construction assemblies in ACCA's Manual-J 8th Edition book. These "types" often have different U-values and assumed temperature differences, which means that they have varying HTM's (Heat Transfer Multipliers). For instance, a sloped ceiling with R38 cavity insulation is referencing group 18A, while a flat ceiling under vented attic references group 16B.

You'll also notice that anytime you're specifying a sloped roof surface using the room properties tab, Wrightsoft is making assumptions about the square footage of these surfaces. When you define a ceiling via the "room properties," flat ceilings use the rooms footprint as the sqft, while sloped ceilings assume a "typical" slope (somewhere around a 6/12, I believe). If your roof is steeper than 6/12, you should use the "ceiling tool" to draw a separate ceiling object on top of your room/building. This will allow you actually define the pitch of the roof, thus being more accurate.

Hope that helps!

Here's a recent post on how Manual-J can lead you to undersized ductwork, if you're not careful. I'd love to know what you think about it. Please comment!

Thanks for the information, I'll start running a few models and see what happens.

In addition to Isaac's response below, if you're insulating the roof deck and encapsulating the attic, be sure to model the ductwork as being within building envelope. This will reduce energy losses through the ducts. 

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