If you are reporting the Limo service as a separate business from the Uber/Lyft, you would enter the miles for each business separately and the program will give the prorated deduction to each business.
From strictly a tax viewpoint, it sounds like they could be combined as one business (assuming the LLC is only one member and has not made an election to be taxed as a corporation). But depending on the details, that could possibly reduce legal liability benefits of the LLC (you would want to consult your business attorney if that is a concern).
