Loren,

One of the notes under Table G3.1.1A of ASHRAE 90.1-2004 states,
"Residential building types include dormitory, hotel, motel, and
multifamily. Residential space types include guest rooms, living
quarters, private living space, and sleeping quarters. Other building
and space types are considered nonresidential." The User's Manual also
says, "If a building has both residential and nonresidential spaces, for
instance a residential tower with retail and restaurants at the base,
then the HVAC system type is determined separately for the residential
and nonresidential portions."

I recently did an energy model for a motel that had first floor retail
spaces, a swimming pool, an indoor parking garage, and a fairly large
lobby. I used realistic systems for these spaces instead of PTACs or
PTHPs. For a different motel I modeled, the nonresidential spaces were
rather insignificant, so I used PTHPs throughout.

Regarding which capacity to use for the EER calculation, I would use
realistic capacities. For example, for the space that needs 40 kBTU/h, I
would assume that there would be two 20 kBTU/h units and use 20 kBTU/h
for the capacity in the EER equation.

I think the decision to use an average EER for all the units is a
judgment call depending on how complex you want your model to be. It's
the usual trade-off between making assumptions to simplify the model or
adding complexity to get more accuracy (presumably).

Sincerely,

Keith Swartz, PE, LEED(r) AP