However, not sure if this is something on your end or something with the way I've done things, but when searching for the PostageApp Node.JS module I created, it had two entries despite only really having one.
I published notificon (an ender compatible library) to the npm registry, but it does not appear on the toolbox. How do I go about submitting packages to the toolbox?
You don't, it is automagically being picked up from npm's couchdb repo. If it's on npm then it is on node-toolbox. If the module has some keywords then the chances are that it will get categorized correctly as well.