My machine has a needle down option for quilting, which automatically brings the presser foot up. If I am concerned about thickness in a very bulky seam, I will sometimes stop one or two stitches into it. This allows all that bulk to relax and when the presser foot comes back down it is automatically on top of the bulk rather than trying to push forward and adjust to the bulk.
Good luck - sometimes each machine has its quirks that you have to learn to work with. This works for me even on my inexpensive brother that I use for classes.