I use it in both top and bobbin so that when I wash the quilt the basting is totally gone. If you use it only in one place and then quilt over that line of stitching several times you will have a problem removing the thread that is not dissolvable. (Remember that your needle can go through, not just over, your basting thread.) I use Vanish from Superior threads.
Edited to say - you didn't say whether you would then be quilting the quilt yourself or giving it to someone else for quilting. That might make a difference. If someone is quilting by hand, they may remove the basting threads before quilting an area. In that case I would probably not use Vanish at all. If they are quilting on a DSM, they will appreciate not having to worry about removing the basting thread after they quilt, but you should be sure that they understand that they will need to wash the quilt to get the basting out.
Last edited by dunster; 03-20-2012 at 08:32 AM.