For all stiffened panel analysis in HyperSizer, the load is applied at the mid-plane of the top facesheet. This is the assumed reference plane for both Nx and Ny load since there is not a single N/A for stiffened panels. A stiffened panel is two dimensional, therefore it technically has two neutral axes - one for Nx load and another for Ny load. The X neutral axis is the location of a plane such that an applied Nx load will induce no bending curvature (kx).
HyperSizer has the ability to zero-out the curvature, which is the same as applying membrane load only at the N/A of the panel. This is accomplished for Non-FEA projects (workspaces) by setting kx, ky and kxy degrees of freedom to "constrained." When the degree of freedom is constrained, reaction (virtual) moments are computed to ensure zero panel curvature. Notice after analyzing the panel, the design-to Mx load = virtual Mx load. Also the design-to curvatures = 0. For more information on the virtual load, see: http://www.hypersizer.com/download.php?type=pdf&file=1021_HyperSizer-Methods-Approach-FBD_Tab_Matrix_Math.pdf
If you out-of plane load causing real bending moments in the panel, you could simply add the real bending moments to the virtual bending moments, then apply this as a user-defined load.
For FEA projects, you could select "Zero Out FEA Computed Moments" on the FBD tab. This will ignore the moments from the FEA and use the HyperSizer-computed virtual moments instead. For more information on this option, see http://hypersizer.com/help/Content/Loads/load-superimposed.php
Let me know if this helps