One way to do it is to baste the top to the batting only, add your embellishments, then baste to the backing and proceed with the quilting. Your knots and tails will then be between the batting and the backing and not show. Be aware that embellishing before quilting makes the quilting process much more difficult, especially if machine quilting, because everything you add must be avoided. The quilting looks much less fluid with this method and does not blend as well with the embellishments.
The other way is, obviously, to sandwich and quilt first, then add your embellishments by hand and bury the knots and tails in the batting. It takes time and care, but I find it results in a much better balance of quilting and embellishments because you can get them closer together and they flow into each other nicely..
Hope that helps, and good luck with whichever you decide.