You can use the includes
option in the yaml to specify a custom addition to your latex header. The yaml part would look like
---
output:
pdf_document:
keep_tex: true
includes:
in_header: header.tex
---
and you need to save a separate file called header.tex
with the following defining your company logo like so:
\usepackage{fancyhdr}
\pagestyle{fancy}
\rhead{\includegraphics[width = .05\textwidth]{logo.png}}
Here I used the fancyhdr
latex package to add the logo, but there are other potential solutions. See here for more options.