Only a few days into RStudio and bookdown, so forgive me if I don't frame the question in the right terms.

As I understand it, preamble.tex deals with things before the \begin{document} execution, so is fine for adding \usepackage{} and whatnot. Is there a comparable place where commands to those packages can be inserted such that they will be put into the LaTeX file in (or by) pandoc?

You are probably looking for before_body .

Usually preamble.tex does indeed go in in_header