Given your info and that you can only have three types of strata I would do the following:
1. Primary Strata = Drought Exposure (Each drought exposure zone will get it’s own set of transition pathways).
2. Secondary Strata = Management Zones (you can define area targets by management zone).
3. Tertiary Strata = All possible combinations of Watersheds, Viewsheds, and Riverine Zone (you can report out results according to this or any other strata type).
If your model is non spatial you will need to specify initial areas by combination of all three ST-Sim Strata Types (under Initial Conditions | Non-spatial). If your model is spatial you will need to input a raster (under Initial Conditions | Spatial) for each of the three ST-Sim strata types where each cell has an integer ID value corresponding to the ID value of the stratum specified in the ST-Sim “Project Properties”.