HyperSizer includes methods for doing laminate-based as well as ply-based analyses. In the laminate based analyses, you can choose AML or a number of other methods (including the Boeing polynomial-based approach) to specify the strain allowables for laminate based strength analysis.
The AML approach is documented in the HyperSizer Methods and Equations (HME) document called, "AID135-159 HyperSizer Material Strength Composites.HME", which is included in the documentation that is installed with HyperSizer. To find this document, open the HyperFinder Technical Document Search from the HyperSizer help menu, and search for "material strength". You can filter the list at the bottom of the HyperFinder form to just show "Methods and Equations" to make it easier.
The Boeing polynomial approach is not documented there, however the principles of specifying the strain allowables are the same. In the AML method, you specify data points relating strain allowable to AML number. In the polynomial approach, you enter coefficients for an equation that relates strain allowable to %0s and %45s.
Let me know if you need further information.