We use Abacus and enter in mileage ASAP. This system allows our bookkeeper to accept the expense as distance traveled quickly and properly account for it (we're accrual).
When we file our taxes (we're cash accounting, as it's often less than accrual) we add a line-item for mileage and report based on our bookkeeping account. Your CPA (tax) should be able to solve this -- I would hire someone. It may cost $1-2K/year, but is very cheap for putting your mind at-ease every year (not to mention the time savings!)