I charge clients for miles over a certain distance do I deduct that from my income or from my overall mileage.

You include the income you charge for mileage and then you claim the mileage as a vehicle expense.

Thank You

You report all your gross income, no matter what you put on the invoice to justify it.

Separately, you can deduct vehicle mileage for work-related travel and transportation (if you are self-employed) according to the rules in IRS publication 463, regardless of whether you billed separately for it.

https://www.irs.gov/pub/irs-pdf/p463.pdf