If all of the actual travel costs are being put on the company credit card, then there is no per diem to pay, the company has paid the actual expenses because they are charged to the company’s credit card and paid by the company.
If owner uses his personal credit card or personal cash for his meals and incidentals, those individual expenses do not go into QuickBooks. The company can pay the owner (or credit his “distributions” account) only for the ME&I (Meals & Incidentals) portion of per diem. Tax law says the lodging for “those related to the employer” cannot be paid per diem. If the owner pays for lodging from his personal funds, he must be reimbursed (or “distributions” account credited) for actual costs incurred. Otherwise, he could just put the lodging on the company credit card and save the reimbursement step.
Here’s the authoritative source: IRS Pub 463 (2011)
Page 6 Heading: “Who can use the standard meal allowance” specifically says self-employed persons are allowed to use it.
Page 30 Heading: “Per Diem and Car Allowances” says that per diem is not allowed for those related to your employer.
Page 31 Heading: “Related to Employer” is defined. One of the tests is if you own 10% or more in value of outstanding stock.
Page 2, Heading: Who should use this publication” employees and self-employed persons.
Page 6, Next to caution “There is no optional standard lodging amount similar to the standard meal allowance, your allowable lodging expense deduction is your actual cost.”