I was getting confused over the Laminate Specification step. Turns out that's what defines stacking sequence in the zone so you have to define that exactly. Although I'm not sure how that works after you move layers around in the sequence manager, but maybe that's just not associative.
I'll definitely hit you up with more as I go!
Hi Henry, here is a quick (but not thorough response): There are actually multiple ways of setting up your stacking order.
I hope this helps!