For sewing over difficult changes in layers, I use a jean-a-ma-jig or presser-foot spacers, aka hump-jumpers.
Sew up to the hump, and with the needle buried raise the foot and insert the spacer behind the needle and manually sew up onto the hump. Sew across the hump. To sew off of the hump, while still on the hump raise the foot with the needle buried, insert the spacer in front of the needle and sew over the drop-off before removing the spacer. Manually climb the hump, over short humps and off the hump.
https://www.amazon.com/Dritz-Jean-Majig-Sewing-Product/dp/B005572NPS/ref=sr_1_2?s=arts-crafts&ie=UTF8&qid=1506068841&sr=1-2&keywords=jean-a-ma-jig