If you wanted shop supplies to be a straight percentage, I think what you'd want to do is setup a bundle. In the bundle you'd have your service at your hourly rate, and a shop supplies item set to hourly at whatever percentage you wanted. Then when you create your invoice, you create it based on hours and the system figures it out.
Whether you want those to display individually - service versus shop items - or as a total amount - project / job - will depend on the way you setup your invoice template.
Hope this helps!
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