Try putting a piece of cardboard (or several) under either the front or the back of the pressure foot until the pressure foot is exactly horizontal as you sew over the thick seams. Often the machine has the power for the needle to go through all the layers, it just doesn't like to do it so well when the pressure foot is not horizontal. There is a little gadget called a hump jumper or something like that which will also help solve the problem.

I realize this is a late post to the question, but am trying to catchup after a family illness. I keep a small hammer in my sewing studio to bang those pesky thick seams into submission. A couple of good wacks with the hammer beats them down an allows my machine to sew over the seams without issue to machine or needles and lessens my stress as well. Have used this method for years and it works for me. Who knew a hammer belonged in your sewing tool box?!