If you're using Sage 50 Quantum, you might be able to make the Labor Burden feature work for you.

In Quantum, when you're allocating hours/wages to jobs, there's a column for "Labor Burden Amount". If you enter the amount of reimbursement that belongs to that job, the amount you enter would debit your Labor Burden Cost of Sales account and credit your Applied Labor Burden account. So in order for that to work, all of your reimbursement fields would have to be set to post to the account designated as the Applied Labor Burden account. So you couldn't have per diem post to one account and mileage post to another account.

You can't enter a Labor Burden Amount without also assigning hours to a job. So if you ever have a reimbursement but not hours for a job (mileage turned in late at end of job) you would have a problem. (You could work around this by allocating an hour to the job along with the reimbursement, and then allocate -1 hours on the next line.)

Of course if you're already using the Labor Burden feature for it's intended use, it would not work well to also use it for this too.

If you can live with those limitation, then you can set your Labor Burden Cost Of Sales account and your Applied Labor Burden Account by going to Maintain > Default Information > Jobs, then go to the Labor Burden tab.

The only other option I can think of would be to include the reimbursements on the payroll check and then use a general journal entry to assign the costs to a job. You could have payroll post them to a holding account and then move them to the final account with the GJE, or you could debit and credit the same account on your GJE but only assign jobs to the debits. I'm just brainstorming here. This would work but the only benefit I can see to this method is that it would save checks. It wouldn't be any less work than what you're doing now.

It is a lot cleaner to write the AP checks.   You can job cost there too. 

We are using Premium Accounting.   Thank you for you answser.

I'm doing it in AP now.   I'd like to include it in their check.   Less work then separate AP checks.