How do you infer what a cross section might look like below sea level? Here is a schematic of a cross section which should represent an anticline:
https://postimg.cc/4HcmmZ26
Below sea level, I have inferred what the units might look like with the dashed lines. As I have interpreted this to be an anticline, it was quite straightforward to understand the possible shape, and by working out true thickness I would represent uniform thickness.
Here is another example of a cross section which should represent a thrust fault system (I may have added these faults at a strange angle, but hopefully this gets my point across):
https://postimg.cc/CRkXJ2Xc
Would I assume these beds are uniformly dipping? How deep should units be represented?
I would say it's reasonable to infer that the strata stay at roughly the same dip angle and thickness in areas not directly visible on the chart you're using.