When you build your "Mock" federal return with Married Filing Separate status you will only put in your income in the federal "Wages and Income" section. This will not include any of his income on your return. Then in the VA state interview in the "Credits Section" you will find the "Low Income Credit" topic. There you will verify/adjust the income so that you spouse's income is not in the calculation for that credit.
Having said that be sure you need to file in VA at all. If you are the spouse of a military member and your spouse is in VA on military orders and you are there only to be with them and his home of record (resident state) is in another state then you can elect to have your resident state match his and your income earned as an employee in VA would not be taxable in VA either.
In other words if your military spouse is not filing in VA due to his military status and VA non-residency then you can do the same.
Here is the VA reference.
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