As always, use care when doing anything with your site, WSI, SQL, etc. I am not an expert and don't guarantee anything I am posting.

If you have an existing order that you would like to credit to an affiliate you can't do so easily through the site. However, if you have WSI you can run a very simple command to do this. Just change 123456 to your order number and change 654321 to your affiliate number to update the records respectively.

C#/VB.NET Code:
<AspDotNetStorefrontImport Verbose="false">
  <Set Table="Orders" ID="123456">
    <AffiliateID>654321</AffiliateID>
  </Set>
</AspDotNetStorefrontImport>