Your mileage between your home and a regular job location (such as your employer's place of business) is always nondeductible commuting mileage.
You should track all of the trips that qualify for your employer's accountable plan separately.
Unlike business miles, what the IRS considers "commuting miles" aren't tax-deductible. If a business mile takes you from one workplace to another, a commuting mile takes you between your home and a workplace.
For your Schedule C / self-employment, trips between business locations and trips outside your commuting area (such as travel away overnight) are deductible.
See IRS Publication 463 for more guidance.
See also this TurboTax tips article for more information on Federal tax laws and employer-accountable plans.
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