When I longarm a quilt with a flange, I always baste it down, just like I baste the edges of the quilt, to ensure it stays out of the way and does not fold over. I'd be furious with a quilter who blithely let it fold and quilted over it like Corinne described.
Sounds to me like you are doing fine, and are too hard on yourself. Sometimes it's difficult to take a step back - look at the overall effect, rather than the quilting in a particular 2" section where you know you had to stop/start. Anyone else is not going to see those, unless there's a horrid wobble in the pattern.