Basically, you will qualify for a partial exclusion of the taxable gain. If the house was your primary residence for 13 of the 24 months required, you'll be able to exclude 13/24 of your gain from taxes. Exactly how the program handles this, depends on where you are reporting the sale in the program. I would expect "Sale of Home (Gain or Loss" under the personal income tab. So when the program asks questions pertaining to the "lived in 2 of last 5" rule, you will indicate that you did live in it for the required time. Then the program will ask how many months each of you lived in it and will figure the percentage of your gain that is excluded based on your input.
Do note that if the program says you don't qualify at all, then it's because you did not indicate to the program that you are active duty military under the Personal Info tab.
