I've read you're questions, and I think the best answer is for you to empty everything you know, and start over. And I don't mean that in a negative way, because I think you already know a lot. When I say start over, I mean, follow everything you read in the documents, and embrace it completely, without letting your preconceived notions or prior habits get in the way.

While you're learning, let Laravel take the drivers seat. When building an App, do it exactly the way Laravel does it. Although Laravel is flexible in many regards, it's only flexible if you're applying it in a way that is consistent with their patterns and principles. Otherwise, Laravel won't budge, and you'll lose many nights trying to let Laravel fit your model.

Now, addressing your concerns, I think a lot of your questions are design related, and I highly recommend you subscribe to Laracasts for most of your answers.