[eluser]Sumon[/eluser]
i am not good one in CI. but from my experience, it's easy but powerful MVC framework. let's share our experience.
First of all you are totally right. User guide is really good starting point.
Difference between library and helper: we can call helper functions directly from anywhere(specially from view) in CI.libraries are useful to implement OOP and re usability of code.
Yes sometimes we create custom config(file inside application/config/)and call them throughout the application.
Next about view i don't understand your question clearly because i am not good in english reading

But i feel, this is the way by which we can implement master page concept. lets share some code
Code:
$data['content'] = 'auth/form_registration_view';
$this->load->view('layout/logged_view', $data);
here logged_view is the master template. to give you and idea, master template=header, left menu, footer.
And finally, in my opinion, we all need to start reading CI user guide with full of patience. user guide is really really helpful one.
Fielder: don't think that, i am an expert. but what i try to do is share some thought with you. i might be wrong at some points. but i am sure you will catch up those and move forward easily.
Welcome to Code Igniter World.