An easy way to SID is to gently spread the seams where you are going to SID so you can maintain a nice stitch in the ditch. If you have color problems variagated thread does help blend more. The object is not to have your SID show on the front of your quilt but there are times when you will have some show regardless of how hard you try to make it perfect.
Another solution many use is to use a decorative stitch that covers each side of the seam but also allows the quilter to still stitch the seamlines. This can be a really pretty effect on your quilt.
You do need to use a walking foot for this keeps both the front and back of your fabric moving together correctly so you won't have any ripples on either side.