What's your state? I suspect KY, because Schedule M is where your active-duty income will be subtracted out from all other claimable income. If that's the case, make sure that you have answered all of the questions in the interview identifying you as active-duty military. Then, make sure that at the end of the W-2 entry screens, that you check the first box on the screen "Do Any of these Uncommon situations Apply?" The First Box is Active Duty income. When you check that box, the income is exempted in KY and appears on Schedule M. Other income still taxable in KY will be reported on the return as normal.
If you are talking about another state, however, please let us know which state that is, so we can assist you.