If your account had Advertisers before the concept of Agencies was introduced, it will be necessary to associate these existing Advertisers with Agencies.
Navigate to the "Agencies" tab in the left toolbar and click into the agency you want add Advertisers to.
Select "Edit Agency" in the top right corner
A modal will appear displaying the Unassigned Advertisers of your Organization. When you see this dialog, select all Advertisers that should be associated with the Agency you are editing by clicking the + icon. Then click Assign to Agency.
About Advertisers that work with multiple Agencies
To reflect real business relationships, companies may be added as Advertisers separately to multiple Agencies. You should create a distinct Advertiser with the same name under any additional Agencies with whom they work.