You will need to create a Subcontract type sub budget. See the Add a Sub Budget user guide article for details.
To apply a different F&A rate to your subcontractor budget, click the F&A tab on the Sub Budget Worksheet, type in the Subcontract F&A Rate, and then select the applicable Subcontract Base Type. You can also choose to use a custom base type.
Refer to your sponsor documentation to make sure you are applying F&A according to their specifications.