You should only bill customers for Billable charges.
Using the Charge reports, you can print charge report that include both Billable and Not Billable charges, but select not to show the Not Billable charges prices and totals, and give the printouts to your customers. This way you can show your customers everything you do, and charge them only for what needs to be charged.
You can also use the Commit QuickBooks Link to generate invoices in QuickBooks based on Billable charges in Commit. The QuickBooks Invoice Creation Wizard includes only Billable charges in the invoice total. You can also add non-billable charges to the invoice for reporting purposes, which will not affect the invoice total.
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