If there is just a small bit of difference between the 2 pieces, and it's a short seam, like 4" or less, you can try sewing with a 'baggy bottom'. In other words the larger piece on the bottom, letting the feed dogs ease the excess fabrics.
Easing is used when there's a fair amount of difference, and/or a long seam. It's often used when joining borders. You measure the quilt top in 3 places, cut your borders to the average length and ease it.
Easing will distribute the excess fabric along the entire length of the seam.
Fold each of the pieces separately, finding the centers. Put a pin in marking this. Now take both ends and fold to the center, finding the quarter distance. Put pins in this spot to mark. If it's a long seam, or there's lots of excess fabric, do it once more finding the eighths. Now pin the 2 pieces together, matching these marked points. Tip: if you use pins with different color heads than the rest of your pins for this, it makes it easier. Treat each section separately, and continue to pin the same manner as you just did for the whole seam. Find the center of the section on each piece and pin it together. Do this until you feel that the seam will be smooth and you can sew it without creating pleats. You might need to rearrange the pins a bit within a section and if you use different pins for the original matching points you know not to move those!