The IRS is still processing my 2019 tax return. Do I continue to make payments on what I owe? We now show a credit. Unsure of what to do.

Your question is unclear.   What are you making payments for?   Do you owe back taxes for which you are on a payment plan?   

Your account would show a credit for the payments you are making which will eventually be applied on the 2019 return whenever they get around to processing it.   If you still have not paid everything you owe then continue to make payments and make sure it is being applied to the 2019 return.