When importing the FEM into a project HyperSizer assumes the stiffener location is in the -z QUAD direction.
If we consider a composite fuselage the tool surface is on the OML. The FEM stress person will orient the QUAD z pointing inboard so that layer 1 in the lay-up is on the tool surface. Subsequent layers will stack inboard. The stress analysis needs z pointing inboard, but HyperSizer would then assume the frames and stiffeners are on the outside of the fuselage (-z).
The QUAD z direction should always point away from the tool surface. HyperSizer should accommodate a user defined direction for frames and stringers to provide the correct analysis solutions for both the loads and stress persons analysis preferences.