It's your quilt, your decision. Use what looks good to you. I base what color thread I use on how much I want the quilting to show. Sometimes the quilting is the star of the show and sometimes it's the patchwork design. I will often take a scrap and do some quilting on that in making my decision. In doing your test piece use some batting and backing too because that will more closely replicate what the finished quilt will look like. This also allows me to decide on the stitch length if I'm not doing free motion and tension setting if I'm using a different color bobbin thread.