I'm totally new to trigger.io and i was wondering if there was a suggested directory for putting files like zepto.js or jquery.js (if I were to use that).
In theory one can place it anywhere within the "src" directory tree. However, I would suggest placing it in the "js" directory. Or even better... to help separate your .js files and 3rd party .js files... place it in a "js/lib" subdirectory. Most (if not all) of the trigger.io examples in their documentation and Github tend to do this.
https://github.com/trigger-corp
One of the great things about developing applications using trigger.io (or Phonegap) is that you can utilize your existing web programming knowledge and best practice.
Still... at the end of the day its up to you to decide how to organize your application. With smaller apps it might not be that important, but as your application grows having a "clean" and manageable structure helps.
Update: In their weather app tutorial they use a "resources" directory.
http://docs.trigger.io/en/v1.3/tutorials/weather/tutorial-2.html