Can one spouse use one bank transfer to CRA for total payment of both spouses who have filed jointly or must they pay seperately?

When you do the bank transfer, you will need to include your social insurance number (SIN) as your CRA account number. So if one person wants to pay for both from the same account, they can, but they would have to do 2 transfers – one for each SIN.

https://www.canada.ca/en/revenue-agency/services/about-canada-revenue-agency-cra/pay-online-banking....