Hello!
Thanks for joining us in the QuickBooks Online community. I can see how having the option to create different markup values for separate customers would be a useful tool.
In Plus-level accounts, turning on the Billable Expenses option allows you to add a markup percentage that's applicable to all billable expenses. The How to enter billable expenses article explains setting up and using that feature in more detail.
The program doesn't have a way assign specific markups to individual customers. As a workaround, you can explore the option of setting up the markup as a Service to add to invoices and transactions that need the markup. Do this by hovering over the Sales option in the left menu and then choosing Products and Services. Click New and then Service to set it up. It's up to you how you set it up, but one option is to create a markup service for each percentage amount (5%, 15%, etc.) you'd like or you could create one simple called Markup. Leave the sales prices blank to manually enter the appropriate dollar amount each time you add it to an invoice.
It would require some manual calculation to determine the dollar amount associated with the percentage each time, but it should work as needed. There are even markup calculators that you can find with a quick Google search. If you're feeling unsure, I encourage you to check in with an accountant. I know getting these numbers right is important.
If you'd like, you can even have your accountant take a look at your QuickBooks account as an accountant user.
Don't hesitate if you have more questions. Enjoy your day.