Start with a MFJ tax return and use https://proconnect.intuit.com/community/tax-filing-status/help/married-filing-jointly-vs-married-fil... to generate the information to create the MFS return. 

If you can file the RDP as if MFJ, use that return to file the state return.

Create two new returns, one for each individual based on the info in the first return.

VERY TEDIOUS.

Here is a lengthy Lacerte article that might help.  I am afraid it still has several warts that have not been removed. Maybe @IntuitBettyJo could put her team on it.

https://proconnect.intuit.com/community/lacerte-tax-discussions/discussion/how-do-i-enter-data-for-r...