Hi Nick, as David mentioned, combine the two levels (and the joist space between them) that have a significant amount of below-grade wall as one level and treat that as a basement. You might even include the joist space above the second level too if a lot of it is below-grade.
But, rather than using Hot2000's Walkout feature, you should use Appendix C of the ERS Hot2000 User Guide to model the walkout.
Stan