For simplicity purposes, I would use a piece of paper to keep track of the estimated tax allocation. Have each spouse claim what was paid under their SSN and have one of them cut a check to the other for any difference. I would not try to get the government(s) involved in that allocation.  I am not sure how the program does that. It should split withholding. 

In Settings > Options, did you set Community Property State to Yes?

Wages and withholding should be split equally. Generally MFS is not advantageous and definitely more work. I did my first in many years for 2020 because of Unemployment.