These are a lot of questions, I suggest skimming through the R packages book [1] for a workflow that many R developers at Posit use, and then ask more specific questions here, should you have any, still.
It does not cover how to install system packages on your chosen Linux distro, I suggest you consult the manuals of you distro for that.
I also suggest you use rig [2] for installing R, and pak [3] for installing R packages. pak will also tell you which system packages you need on many Linux distros, or it can even automatically install them, depending on your setup.
[1] https://r-pkgs.org/
[2] GitHub - r-lib/rig: The R Installation Manager
[3] All about installing pak. — Installing pak • pak