For debugging your Meteor's server side app, just set the Debug flag, launch a Node-Inspector and open your Chrome navigator on the URL provided by Node-Inspector. Basically, it covers the Step 2 of the Meteorpedia article on debugging.
For launching Meteor so that it uses an alternate MongoDB instance, you simply specify the access to this instance. Default installation of MongoDB are usually accessed via
mongodb://localhost:27017. Revert back to the classical MongoDB within Meteor, blank the content of the Mongo URL input field.