I find that no matter what theme I apply to the shelf itself, any sub-docks do not reflect that theme. I haven't been able to find any option that asks to apply themes to sub-docks or indicates a default theme for sub-docks.

How do I go about matching the overall theme and the sub-dock theme?

Basically, you can right-click on the shelf icon representing the sub-dock, select "dock properties" and then select the theme of your preference.
Theoretically, any new sub-docks you create should follow the shelf's theme. I'm not sure what happens when you change the main dock's theme *after* creating the sub-dock, but...