Answering my own question:
Thanks mnel for the tip. Just use knit_theme: you use the command knit_themein the R Sweave document, similar to how you put code snippets.
eg:.
\documentclass[12pt,a4paper,final]{article}
<<adjust-preamble, include=FALSE>>=
knit_theme$set("seashell")
@
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
\usepackage{savetrees}
\begin{document}
etc.
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