Official comment
Hi Matt,
That is a good question.
If you are performing a block load calculation I would recommend creating a single room with location = Below Grade, then entering 3ft for the height below grade and 5ft for the height above grade. This will be used to determine your infiltration calculations.
You can then create a below grade wall that is entirely below grade (match the ceiling hight to the below grade portion) and an above grade wall that is entirely above grade (match the ceiling height to the above grade portion). This will allow you the flexibility to have different insulation values for each. The only problem is the tables in the Manual J book are listed in 2ft increments, so you will not be able to select 3ft below grade (you will need to choose between 2 and 4).
Best Regards
Bill