I know that there is one side of the ditch that is easier to stitch than the other; I can't remember which one, you can test it. I know that some people use a very small zig zag stitch so they say it doesn't show as badly if it's crooked or you can chose a stitch w/a wavy line to make it less noticable. Hope this helps
there is also a SID foot that has a blade down the middle to help you stay in the ditch; it spreads the seam open enough to allow it to work better. Have you tried pressing the seams really good first to make sure they are laying flat.