We no longer recommend forking (modifying Blockly itself) to add features like this, but it should be reasonably straightforward to do something similar in the form of a plugin like the existing
Continuous Toolbox plugin (which does not support checkboxes but does demonstrate how to replace the built-in toolbox with one with extra features).
Alternatively, if you're not in a hurry you could wait and let us do much of this work for you: it happens that some of my Blockly team colleagues are in fact working on unforking Scratch Blocks—that is to say, rewriting it to use the current mainline version of Blockly, with all of its extra features (like checkboxes in the toolbox) implemented as plugins. I don't know what the timeline on that work is, but it will eventually result in the publication of a new version of Scratch Blocks with this checkbox feature provided plugin-style (though probably not as a neatly packaged, separately published plugin like the one mentioned above).
Best wishes,
Christopher