I don't see an option for that. This is utilizing their Free version of connectwise control so there is only the one main account. I do work for a company that uses the paid one, and I know they have multiple accounts - but there it's just one mfa/phone per account as well.
We have a lot of customers set up on Duo MFA for various rdp logins, for the company I work for. In their setup each 'account' can have multiple phones registered and it works great.
Customer support service by UserEcho