I only take two stitches after I bring up my bobbin thread, and by the time I take both threads to the back, and take them back through the same hole they just came through, that tiny knot completely disappears into the layers just as if I'd been handquilting. Just keep practicing and you'll get it perfect before you know it! :)
There are times when I choose not to do it that way though, and just back stitch a bit like you said you do. Like when I have a kabillion starts and stops in one block. That's just too many thread ends to have to bury!! At those times I just backstitch and go, then slice both the top and bobbin threads close to the quilt top. :D