When creating a quote/contract for an Advertiser that uses an Agency, the Agency will prepopulate on the quote/contract.
*Be sure you have selected the Agency used by the Advertiser on the Advertiser record for the Agency to prepopulate on the quote/contract. (see picture below)
When using the Agency on the quote/contract, the contract will be grossed up by the commission rate that appears on the Agency record. (see picture below)
*By default, Agency appears on quote/contract with commission rate with billing to the Agency.