Sometimes when joining pieced edges, the top and bottom layer are uneven - one side is longer than the other. When this happens, always sew with the longer layer on top. Line up the edges as they should be, finger pin, and sew a couple of stitches to anchor. Then finger pin the next intersection as it should line up, and ease the top (longer) layer by slightly stretching the fabric as you stitch until the bottom and top are even. Do the same thing for each intersection, and at the end of the row of stitching. I've illustrated the process below.
Pressing is an important step. As you can see in the first photo below, there is still some fullness on the top layer. Press seam flat, and then press open. The second photo shows the resulting matching intersection, and flat seam.
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Happy Sewing ♥