You can use different colours of thread in your bobbin and top. Thread choice is part of the quilting and whether you want your stitches to disappear or create a picture.
A good walking foot has made the difference for me with puckers. If I see something forming that might be a pucker, I simply stop and smooth out the area I'm sewing and that seems to fix things.
If you're using a domestic machine for this, another thing I have heard is that it's better to "stuff" the quilt rather than rolling. I've done both, and use both depending on what and how I am quilting. If I'm stippling, I will roll the areas not being quilted, but if I'm SITD, I stuff.