I've updated this quite a bit and removed the original option to use a markdown only file. This current method is my preferred option, and requires only a single .Rmd and a formatted .tex file. This has been kindly adapted from svmiller great blog post and source code.
Open the Rmd, edit as required. Then knit to pdf. Simple, clean, adaptable.
To use, simply edit the Rmarkdown file using the editor of choice (RStudio is native and effective), then knit to pdf.