Using the new GCSE code like so:
// google custom search engine for the whole site
(function() {
var cx
With Custom Search Element v1 it can be done relatively easy:
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Demo: Multiple Google CSE on the same page
http://box.galeksic.com/cse.multiple-on-same-page/
JavaScript API Reference (v1)
https://developers.google.com/custom-search/docs/js/cselement-reference
I've tried with v2, but wasn't very successful.