application.js

// This happens in the main application

'use strict';

var base = require('cah-base-model');
base.init(Bookshelf.PG);

var userModule = require('users-module');
userModule.initModels(base);

var User = userModule.models.User;

var myUser = new User.Model({ id : 1 }).fetch();

base-model.js

// This is its own module

'use strict';

var Model;
var Collection;

exports.init = function(bookshelf) {
   Model = bookshelf.Model.extend(...);
   Collection = bookshelf.Collection.extend(...);
};

exports.Model = Model;
exports.Collection = Collection;

user-model.js

// This is a model inside of a module

var Model;
var Collection;

exports.init = function(base) {
  Model = base.Model.extend({}, {});
  Collection = base.Model.extend({}, {});
};

exports.Model = Model;
exports.Collection = Collection;