What's the best way of learning a system with minimal documentation?

System was made in the 90s. There are 3 people alive who understand how it works. None of them are in my company. My boss also doesn't know how it works but has been using it for 20 years. He's also out of the office most days. I'm brand new to this. Been trying to use the documentation but it assumes you have a basic knowledge of our system.

How would you go about learning something you knew nothing about? Is there an agreed upon procedure, or a best practice? Are there tools I should be using? Thanks!