Note: In this example we are setting a Markup within a quote but the same steps apply for within an invoice.
Step 1: Select line items > Selected Items drop down > Set Markup
As shown below we have selected a section within a quote and gone to Seleted Items and Set Markup.
Step 2: Enter the markup percent and OK
The markup has been set
To view the markup select Show Buy Price & Markup under View Options.
Only you will be able to view the markup, to make sure your customer can't see the markup go into options and columns to hide, see the article; How do the printing options work in Invoices and Quotes.