Using HAP i would deal with your scenario in the following manner.
Basement 1 - shares a common floor / ceiling with Basement 2 and common floor / ceiling with Ground level.
I would treat Basement 1 floor and ceilings as partions, in fact i would treat all walls this way too, just choosing for floor tab (above conditioned space).
Basement 2 - shares a common floor / ceilgin with Basement 1 but has a slab below grade.
I would treat all the walls and the ceiling to basement 2 as partitions and enter the slab below grade details for this level into the floor tab.
One way of dealing with your dilemma..