Although I am confused as to what it means when people say certain elements "exist" as atoms or diatomic molecules. Could you explain with reference to the definition of a substance that we have gone over? Thank you very much in advance.
Back to marbles - imagine all green marbles are called "nitrogen atoms". Then, if you have a collection of green marbles, you have some nitrogen, or you have some nitrogen atoms. Now, thing is, these green marbles have tendency to connect to each other, so that they look like kind of a dumbbell. We call these dumbbells "nitrogen" as well. When it matters and we need precision we should name them specifically "nitrogen atoms" or "nitrogen molecules", but most often we will just say "nitrogen", as the exact form is typically obvious from the context.
Separate nitrogen atoms (while they can exist in some exotic conditions) are very rare, they have very strong tendency to combine into molecules. So nitrogen as a "substance" (collection of objects) will be almost always collection of nitrogen molecules. We also often say "nitrogen" when we really mean "gas made of nitrogen molecules" - again, in most cases context gives the clues. Whenever in doubt you can always use more descriptive name (thus "atomic nitrogen gas" will be perfectly understood and unambiguous, although every chemist will think about gas of high temperature and/or very low pressure, as these are the only conditions where such gas is reasonably stable).