Welcome to R Markdown ecosystem then ! Glad you find it useful.
Did you already looked at documentation to get a sense on how it all works ?
You should find the answer about how to use bibliography using .bib file inside R Markdown document in the books above.
You mean another bib file with only the referenced used ? If so, then it is not standard by Pandoc or some R packages should probably allow you to do that. rmarkdown itself will use Pandoc to include the bibliography inside the resulting document, in the correct format.
This would be something external to rmarkdown and knitr. Publishing workflow won't be part of the tool directly. bookdown has helper to publish books to bookdown.org.
If you are new to R Markdown, you could also have a look at new project Quarto
It is based on R Markdown experience but not made in R and it targets broader usage for non R content also.
There is a publishing option built-in to several place using quarto publish
Regarding the above question, it will be the same answer.
Thanks for the reply. I looked through the documentation but the answer still eluded me, but I didn't have the cookbook which does go more in-depth into how the files are generated and how to customise the process.