Do we really need to put the historical thinking skill throughout the essay? I know we have to address it in the thesis, but it isn’t really referenced in the rubric.
You should definitely use a historical thinking skill to frame your thesis and the overall essay, but there is no point associated with it so you technically do not have to follow it throughout. However, your thesis will likely be based on one of these, and thus your argument should be as well.
Understanding that the question is causation, compare and contrast, or CCOT helps you organize your essay and formulate and strengthen your arguments with precision. So, yes, it should be reflected that you understand what kind of question it is by how you address it in your thesis (because this lets the reader know you know), but as important though, this really does set you up to properly analyze the documents and support your arguments based on the kind of argument you are making, because proving cause is a different tact than comparing or contrasting.