I really wouldn't use the clear thread in the bobbin for embroidery. For one, to wind a bobbin with it, you have to go really slow or the thread will stretch. I did wind one once and I couldn't get the plastic bobbin off the winder pin. I had to break it off.
I use Bottom Line in the bobbin when doing embroidery work. It is made for things like this. I match the thread color as close as I can with the top color. No problems with the bobbin showing through. Botton Line is a 60wt thread and very nice to work with. I have used it also for piecing and quilting a large quilt with.