Get your taxes done using TurboTax

-Does TurboTax accurately determine which filing status is better for you or, in some cases, do you have to complete a test return to determine which filing status is better.

• Based on the Personal information you've entered, TurboTax will suggest a filing status.  Selecting Married Filing Jointly, vs. Married Filing Separately is a decision you will have to make.
• Yes, you would have to do a test return to determine your personal best option.  I would suggest the Desktop version, because you can do up to 5 tax returns on it.

-If you switch from filing jointly to separately, can you still upload prior year joint return to new separate return so that TurboTax can transfer the relevant information, or do you have to manually input everything?  The same applies vice versa, if you decide in future years to return to filing a joint return, can you upload prior separate returns into new TurboTax joint return so that relevant information is transferred?

• Yes, you can upload a prior return, but it will be the Married Jointly return.  Please see this link How do I switch from filing jointly to filing separately?
• No, there is no way to combine two married filing separately returns into a married filing jointly return.

Basically, does TurboTax handle the transitions well, especially in cases where there is more than a basic tax return: capital loss carryovers, rental property issues, property taxes, etc.  

• Yes, however, you will have to do the work of allocated each item.

What I'm discovering so far is that if you want to start a new Married Filing Separate return, you either have to start an entire new return without transferring the information (system won't allow me to transfer in this case) or, you have to manually remove the other spouse info as you come to it. 

• That is essentially true.  The link above may provide some shortcuts.

This seems like it could be a recipe for a problem, especially when current returns depend on prior year returns.

• Although you do have to exercise caution, it is a doable task.  
• One note that I wish to emphasize is that if one spouses uses Itemized Deductions, both must use them.  One cannot use Itemized and the other the Standard Deduction.