Hi @realhiphop! Welcome!
On question 1, are you asking about how you would cite the source for your tables in your report text? Or how you cause the external scripts to run so that the data becomes available for your report code to beautify and present?
And can you explain a bit more about your workflow? Are your external data in a database? Some CSVs? Coming from a third-party API?
The question of how to incorporate data into an R Markdown workflow comes up a lot and there's no one right answer. Here's a previous discussion that might be of interest, now or later:
Your question #2 is a good one, and I think a bit different from looking at synthetic examples (those are also important though!). But I fear people with relevant projects to share might not find this post because the title is fairly uninformative. Maybe considering editing it to focus on your specific questions? "Newbie" is often in the eye of the beholder anyway! 