Question

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

Answer 1

I would say "it."
Because it's non-living.

Answer 2

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.