There are two ways to create the refinements lables that show up in the custom search pane, first by using the Control Panel, and second by editing and then submitting a specialised XML file.
The latter allows you more control over the end result.
# Using the Control Panel
On the Refinements page of the control panel, click "Add Refinement". Specify the refinement name (such as "Product Details"). Specify your query addition in the box labeled "Word(s) to add to the search query". Select "Give priority to labeled sites" (to set your refinement label to "BOOST" mode). (Note: The "Search only selected sites" setting, which selects "FILTER" mode, would not be suitable in this case, because you're not associating labels with annotation subsets for filtering purposes.)
# Using a CSE Annotations File
If you prefer to define your refinements by editing the XML specification (context file) of your CSE: * Define your refinements in "Facet" & "FacetItem" XML elements as described in documentation. * In each rewrite refinement's "Label" element, set the "mode" attribute to "BOOST". * Specify your query addition in a "Rewrite" element.
See XML examples under "Creating Refinement Labels" and "Appending Search Queries with Refinement Labels" at: code.google.com 
and
code.google.com
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 Custom Search XML Annotations file.