For the skipped stitches, make sure everything is threaded correctly. Then make sure your tension is correct, lastly, make sure you are using the correct needle size. Remember that the quilt sandwich is much thicker than when piecing and that necessitates a different needle. There are needles specifically for quilting, but some folks use a topstitch needle. I am sure some of the folks on here can help more, but that is what came to mind.
As for stitching in the ditch, try a matching thread, and as Margie said, line up your presser foot so you are stitching just a little to the side of the seam. Go to You Tube search stitch in the ditch, and they are tons of videos to see how to do it. Good luck.