I'm making a homebrew background with 2 contact charts to roll on, similar to the Dimir Operative background from the Guldmasters' guide to Ravnica, but I don’t see a way to add it, how would i do this?

You would add each contact chart separately by selecting a different “contact type.” All of the “contact” contacts go on one chart, and all of the “non-contact” contacts go on the second chart. That’s how those M:tG backgrounds like Dimir Operative were programmed.

but what if my person has two contacts and an enemy? they would have 1 contact, 1 non-contact, and 1...

They would choose two contacts from the Contact list just like the Dimir Operative.

thanks!