When writing about a company in a paper, do I refer to the company as "they" or "it"? ... ?

It depends on what you are referring to.

If you are talking about the company itself, for example, when it was founded, you will say it - It was founded in 1993.

However, if you are talking about its employees, then you should use they.

I would say "it."

Because it's non-living.