Hello@afproduces
You need to set up a separate account to track the per diem. Go to Settings --> Chart of Accounts --> New, and create an income account named something like "Non-Taxable Per Diem." When you receive the per diem payment, enter it as income, but be sure to select the new non-taxable per diem account you just created. This will allow you to keep it separate from your regular taxable income.
Since this is considered non-taxable in your industry, you can simply leave it off any tax categories or make sure that it's excluded when you run tax-related reports.
Hope it helps