Well Kate, I'm sorry to hear about your frustration. It sounds like you really care about your spin class and instructor.

For me, I just do what feels like real cycling to me... when I'm a spin class. If I wouldn't do it on the road, I won't do it in a spin class. If I'm going to hurt myself... aka: my knees.. I don't do it.

Let's face it, unless we live where there are huge hills and we don't have a triple... we are RARELY going to mash the pedals with extremely low cadence, sitting down. But, spin instructors tell people to do it all the time

Good luck on getting it all worked out... but I think if you just do what feels right, it will all work itself out.