Joshua, I am sorry that we dropped the ball on this one. A couple weeks ago we have made some changes in our script which should make it "conflict proof".
The way it works now, if there is a jQuery include present before you include box.js, and its version is greater than 1.2.3 (which is the jQuery version we use), then our jQuery object is only referenced as ejejc_jQuery and your jQuery object is available as jQuery.
You can also "force" this behavior by setting EJEJC_PLAYNICE=true; in EJEJC_config function.
All the conflict resolution code can now be plainly seen in box.js.
Do let us know if you still face an issue and we'll promptly address it.