Alfred,
While feeding the 2 layers of material to my machine, I hold the material together at each upcoming intersection with my left hand. If it looks like the top piece of the material is getting a little slack in it before getting to the seam, then I use the point of a seam ripper in my right hand to ease the material under the foot a little at a time until the top material is flat again. so that when I get to the intersection everything is lining up just fine. Hope that helps! It works for me. Maybe someone else will have another idea for you. :D
Pam