I have two taxpayers, for whom I prepared individual tax return for 2018.  They got married in 2019. In order to file Married filing separately, do I prepare their individual 2019 tax returns as if they were single taxpayers but check off the box "Married filing separately"? I'm assuming that the program will calculate all the relevant deductions correctly.

The reason I'm asking is that I prepared their return both ways and the "married filing separately" actually gives them better results.  I find that unbelievable.  Any comments?