I use them for handpiecing and applique. My bobbin thread is always Bottom Line which my Jems will not take as a top thread, otherwise I might use it up as a top thread.
Rarely do my top thread and bobbin match; I tend to use gray, cream or ivory for all my machine work. If it's a very dark fabric quilt I'll use a dark Aurifil on top and a dark Bottom Line in the bobbin, doesn't matter what the actual colour is as long as it's dark.