What are scientists exactly seeing when they study cells. Can they see every intricate detail of a cell or just an outline of it. Can an atom be seen in its intricate detail? I am curious since I have run across in research that microbes are viewed as just chemical reactions, life forms are just animated chemical reactions, atoms reacting is how organisms came into existence, etc. The impression I am getting is that science have many conclusions based on just seeing the reactions and have very little understanding of the initiation processes that gives it facts.

It depends on the microscope. With light microscopes you are limited to things about the size of visible wavelengths, regardless of how good the microscope is. Then there's electron microscopes and various other fancier and more expensive ones that can see even smaller -- but with most of these you have to kill what you're looking at.

Microscopic studies is an important tool for the researcher to found evidence. I agree that it really depends on the microsoft. Just look for some great science examples research.