Yes, you should be asked the dates you lived in NJ and also the dates your spouse lived in NJ. Her total income (or her total tax due on her income) will be adjusted according to the % she lived in NJ (different states handle it differently, but the net out is the same).
It would be easier to see the calculations in TurboTax Desktop. You would then be able to review/edit directly on the forms.
The only way I could see using TurboTax Online is for your MFJ Federal and New Jersey returns.
You wife could open her own TurboTax Online account to file as MFS for Maryland.
Unfortunately, you may need to do some calculations. The % of any other income (besides W-2) and deductions is split 50% for each of you, and then the % of that 50% of these attributable to Maryland.
Click this link some info on Allocating Income as a Part-Year Resident that may help.
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