create.js

require('./schema');

var m = require('mongoose');

var Model = m.model('mymodel');


var model = new Model({
	name: 'test',
	elements: [{
		name: 'schemafree'
	}]
});

model.save(function(err) {
	if (err) {
		console.log(err);
	}
});

modify.js

require('./schema');

var m = require('mongoose');

var Model = m.model('mymodel');

Model.findOne({}, function(err, model) {
	var level3 = model.elements[0].name = 'schemafree updated';
	model.save(function(err) {
		console.log(err);
	});
});

schema.js

var m = require('mongoose');

m.connect('mongodb://localhost/mongoose');


var Schema = new m.Schema({
	name: String,
	elements: {}
});

m.model('mymodel', Schema);