Markup covers company overhead and profit. Estimators apply it after they total the direct costs.
Markup and margin are different numbers. A job that costs 100 and sells for 125 has a 25 percent markup. The same job has a 20 percent margin, because margin is a percent of the price.
Know which one your company means when it sets a target. Mixing them up underprices every bid. On change orders, the contract may limit the markup you can charge, so check it before you price a change.