To add a Percent Markup, click on the Totals / Markups option on the Summary Sheet toolbar. Next, right mouse click on any row in the Totals / Markups panel and select Insert New Below or Insert New Above. This will bring up the Add Markup window. In the Add Markup Window, type in a description for the new markup and then choose Percent for the markup Type.
If you had inserted a Subtotal above the percentage markup, the percentage markup would use the previous subtotal as the basis for calculating the amount. If you had inserted a subtotal above the percent markup, but you still wish the markup to be based on the project "net total", then you can check the box labeled Applies to Net Total.
The next step is to enter the percentage for the Percent markup. After entering the percentage you can then choose how the markup amount is to be spread across the bid packages in the project.
If you choose to limit how the basis for the Percent markup and how it is to be spread across the project, click on the Limit to WBSes option towards the bottom of the markup page. Next, determine which WBS the markup should be spread to. For example, if you choose Alternate, you could limit the percentage basis to specific alternates. For example, you may want to limit the percent type markup to just the costs associated with the base bid, as demonstrated in the screenshot below: