@joshuabarksatlcs has given some very useful input of the process.

@Gene O I'll just do the easy part and state the obvious. Lacerte's (and similarly for ProConnect Tax, which uses the same engine) MFJ/MFS comparison is very handy but less than perfect, especially for certain items that may not be easily split based on just TSJ coding.  You probably have already double checked all the details before posting this.  But in case you have not, do a thorough review of all the line items and satisfy yourself that MFS does yield better results before spending your time preparing the separate returns.