Are you pulling the bobbin thread up when you start? If you don't, you will get the knots. The needle hitting the throat plate is because you are moving the fabric too fast. Not sure about the bobbin thread since I didn't have that issue. Keep the speed of the machine faster than the speed you move the quilt around. It takes lots of practice.
What foot are you using? I didn't like the R foot that came with it, so I got a spring foot with the clear base. I saw instant improvement when I started using it.