I see what you mean by losing something. Definately do the multiply layer thing so your lines aren't lost. Also, I would consider darkening your lines so they aren't lost in the color.
Maybe you should try to draw directly into the computer for a while. When you get your flow back the same as you would with a pencil (this is provided you have a tablet) then your painting will come looser and easier. Mostly, it's just going to take some getting used to no matter what you do. I know it took me a long time to transition from pencil and paper to a tablet. Keep at it. (Your linework is awesome by the way.)
An open mouth and an open mind go hand in hand. - me