You can create refinement labels and tag sites with them in the Refinements Tab of the control panel, but you can have greater control over the ranking if you are using the Search Annotations File - developers.google.com 
An annotations file is simply a list of annotations. Each annotation has two components: * the site * associated labels.
The label tells Custom Search how to handle a site; that is, whether a site should be included, excluded, promoted, or demoted. In the context file, you define labels; in the annotations file, you tag sites with the appropriate labels.
As with the search engine labels, you define refinement labels in the context file and apply them to sites in the Search Annotations File.
Search Annotations Files can be in any of the following formats: * Outline Processor Markup Language (OPML) * Text files with tab-separated values (TSV) * Custom Search XML
# No more programatic uploads
You can no longer programatically add or remove annotations the Custom Search Enigne. Instead you have to do this manually using the Advanced Tab of the Control Panel.
The only api available now is the one that allows you to search - developers.google.com
# See also - Editing Custom Search Files - Search Annotations File