I nearly always use a different color bobbin thread than the top thread on my Avante, and never have any problem with it coming through, unless it is black or red in the bobbin and white on top. And I find it does sink into the quilt when washed.
I did see at one time that Joann had a wide fleece. I have used fleece for backing, but found it sagged when on the longarm. I just don't like minkee, don't like the feel of it in my hands so I don't use it at all, too linty also to suit me. But flannel backings are great. I used a flannel sheet for one I did for my son.