If I am married, filing jointly, and living with my spouse, do I combine both of our Minnesota Certificates of Rent Paid into a single electronic submission?

No.  You will enter each individually.  As you proceed through your Minnesota return and select you wish to report a renters credit, there'll be a Certificate of Rent Paid Worksheet to fill out. You will enter the first certificate information here. ‌Once this is complete, you will see a summary page. Here you have the opportunity to enter a second certificate.  Please see the screenshot below.