Suzanne, the easiest way is to simplify the problem - just report the mileage under one business. It will make no difference in your taxable income or income subject to self-employment.
In my case, my wife and I have separate companies and file separate/Married. I deduct mileage between clients for checking the backflow devices for their in-ground sprinkler systems. Her business focuses on starting up the sprinkler systems in the spring and winterizing in the fall.
How do we separate the mileage between our two companies?
If your concern is that you both used the same vehicle, it is ok to report the same vehicle if you are taking the standard mileage deduction and only reporting your portion. As long as the costs are not counted twice, it is allowable.
Since your income will be entered in separate TurboTax programs when filing Married Filing Separate, only enter your portion of the business miles. Your wife can use the same vehicle and only enter her portion of the business miles.
See Can I deduct mileage? for more details.