Line up the seams as you go, and they will all fit. Seam should nest, one point toward you and one point away. I like to put a pin at each seam if it is important that they match exactly. If the bottom seam allowance is going into the machine first (pointing away from you) it is very important to put a pin in this seam allowance to keep that seam from flipping back toward you.
I try to line up the seams so that the top seam allowance is the one that goes into the machine first. The bottom one will follow. I can see that the top seam is going into the machine the correct way, and very often use a wooden skewer or dowel or toothpick, etc. to make this one behave.