I want to encourage you. I, too, started with QAYG thinking that it was the easiest place to start. I took Marti Mitchell's class on Craftsy where she taught the principles of QAYG. Everyone has to start somewhere and I applaud you for starting. It can be a struggle to produce that first quilt, but it opens the way to some really wonderful experiences. I think I am now on my 15th quilt and have plans ahead for many more. They should call it LEARN AS YOU GO!
Those joining strips go right side to right side, sandwiching the quilt top, batting and backing in between.
If the corner squares are a problem, forget about them, but don't forget that leaving them out will necessitate cutting changes to compensate for their omission.
I think the "quilt as desired" directions may be a way of saying that you need more quilting than they have included in their directions. Yes, you can sew on top of the layers. You can use crosshatch or straight stitch, but be careful that you use a walking foot to avoid puckering up your quilt backing.
The best suggestion I have for you is to stop agonizing and watch some of the good you-tube videos that are free and available . You could start with this:
https://www.youtube.com/watch?v=l8kyurCw8-g
Whatever you do, don't give up!