I am using markdown & pandoc for scientific writing, I know I can change margins of the final pdf using
Set margin size when converting from Markdown to PDF with pa
There is maybe an easy way: generate a file with the packages we need
\usepackage{setspace}
\doublespacing
\usepackage[vmargin=1in,hmargin=1in]{geometry}
\usepackage{lineno}
\linenumbers
I named it options.sty. And use the -H FILE option that includes the content of the FILE at the end of the preamble. (as used in https://github.com/karthikram/smb_git)
pandoc -H options.sty --bibliography mypaper.bib mypaper.md -o mypaper.pdf
The advantage is that we don't need to edit the template. To add linenumbers, change margins, and set spacing it works.