Charge by the hour. Usual studio rates are approx 60-100 pound per hour, Depends on the client. You wouldn't charge a person looking for bday card the same as a pharma group that come in looking for something specific.
Mark up on print - usually 3x the quote you get on trade prices. Don't forget you're getting trade prices, the usual punter does not get these prices and it's still cheaper then if they went themselves. Plus it covers you for any reprints that may be your fault.