For starters, as the sole owner of the business, if it's a sole proprietorship or single member LLC, then you flat out can not be an employee of that business. Under no circumstances will you ever issue yourself a W-2, a 1099-MISC, or any other type of tax reporting document with no exceptions.
All business vehicle expenses are claimed on the SCH C, and nowhere else with no exceptions. In the program, you'll deal with all vehicle expenses under the Business Expenses section in the one labeled Vehicle Business Expenses.
