Welcome to Guitar tricks..
Everyone has a different learning curve. Fundamentals 1 is pretty much what you need to communicate with other and your instrument. Like most skills the foundation is the most important. As you become more comfortable with the learning process here you will speed up. Not to say you won't hit speed bumps.
Takes note when thing are a bit hard to grasp ask an instructor to clarify, or post question in forum. Take note of what lesson you are on so people can pin-point where you are at. Post that with your question.
Your home work is your practice.. What ever lesson your on. Work on clarity, timing, practice practice practice..
Guitar and amp setting are totally up to you. Your taste, your music. When you get to where you are learning song and styles, you can then work on setting.
I change setting just so that repetition is less boring. I recommend not using effects for a while. At least that's what my mentor suggested to me.
Progress feedback. Post an audio or video recording to the lesson instructor or the "LISTENING FORUM"