It is physically impossible to import from more than one prior year return. Doesn't matter if you use the online version or the CD version of TurboTax.
For a married couple to file separate returns will almost *always* cost you more tax-wise. When a married couple files separate, they *automatically* disqualify themselves for deductions and credits they would otherwise qualify for if they filed joint. The exceptions are so rare, I won't bother listing them here, as if one of the exceptions did apply to you, you'd be paying someone else to do your taxes (because you'd be that rich) and not wasting your time doing them yourselves.
For the first year of marriage it is generally best that you not import from either tax return. Instead, you should print out each prior year return so that you can manually enter any "carryover" information into the new, first joint return and start your married tax life with a "fresh start) so to speak.
