pressing seams open and flat before piecing top together is the thing to do.
perhaps you could lay your quilt on the floor and place a piece of wood and hit those seam bumps with a hammer to help them lay a bit more flat. I used to use hump jumpers long ago in sewing but haven't done so in years. Otherwise plan your quilting to go around those obstacles with the quilting design. you might break a needle if you continue to try and stitch over bumps.