Well, you don’t rotoscope with those tools – for that you use articulated masks.
But if you want to paint, you do it directly on the layer in the Layer window. If you want the layer to contain one or all of the layers below it, precompose them. If you’re opening the layer window and just seeing transparency instead of the contents of the layer, make sure Paint On Transparent is off in the Paint effect control.
If you don’t need to clone, you can paint directly in the Comp window with the Vector Paint effect.
Another approach is to open the layer window and position it next to the comp window. Paint in the Layer window and see the results over your other layers in the Comp window.
Joey Foreman
Editor/Animator
Nowhere Productions, Athens, GA