Well I use either sweats or during winter I use a fleece wader liner, both work well for the back of the knees. I went last weekend without, just shorts under the waders, and now daily I am reminded why I wear something under the waders.

As for flipping, all my rods are 6' - 6'6", anything longer I found to long to handle from a tube. 6'6" works well for me when flipping in the tube.