Hi Nach,
I've just started doing the same. I'm starting to write up a tutorial/blog which should go over some concepts and ways to use the closure set of tools to build web applications. The blog is on
http://rhysbrettbowen.com. I've only just started it but I'm going to try and do a post per day to get some good content on it in the next month or so.
I've written an MVC, you should definitely use the pattern even if you don't use my framework. You can find it on
https://github.com/rhysbrettbowen/goog.mvc, there is a bit of documentation there which should hopefully be enough to get you started, and some tests - though I need to go through and write more. It's nearing v1 and all should be buttoned down in the next week or two.
Folder structure can also be important. At the moment I'm splitting up in to 3 files: js, styles & templates. So the GSS goes in styles and my soy templates go in to templates. I've also got a folder called strings under templates which I use for translatable strings in the templates. Under js I've got app which I use for the main file and other classes that the whole program can access (like the mediator), api which is for communication with servers, control for all the controls, models for the models with two subfolders: sync for the model syncs and schema where I hold the schemas for the models. And last I've got a ui folder where I put in the ui.components for the page and areas not associated with a model with a subfolder of widget where I keep reusable UI bits (things like image gallery or customized text editor).
If you just stay tuned to the blog I should start diving in to the MVC library probably on friday and try to show good patterns of how to use it. If there are any questions just ask - I'm always happy to get a bit of input to improve what is there.