I think the use of "skeletons" is extremely common, and largely recommended for artists of all skill levels.
By "noisy", do you just mean that you find you have too many line and start to get confused? It sounds like you may be drawing the initial skeleton too dark. Have you ever done practice exercises for controlling the darkness you are laying down with your pencil? You may find that this will help you to start feather-light, so that your later lines are easier to lay on top of the skeleton without creating a visual cacophony. Plus, they're really relaxing.
Gradient exercises are simple to do. Basically, draw 5 boxes, about 1 inch by inch, on a piece of paper. Fill in the boxes from the darkest your pencil can possibly create, to the lightest it can possibly create. It should take 5 minutes tops. Then go on to do your normal drawing practice.
The next day, draw 6 1x1 boxes, and fill them in from the darkest to the lightest. The following day, draw 7 boxes. The idea is to get ever finer control over the pressure that you put on your pencil, until you can create 20 or more distinct shades of grey with a single pencil.
About never quite putting them in the anatomically correct place -- this is just practice, and the fact that you are able to look at your drawing and say, this is not quite right, shows progress! Mentally review each of your drawings to see where you went wrong, and just make a mental note of it for the future.
The other thing about working really light, starting with your skeleton, bubbling in major regions, and then going back and doing your sketch on top of it all, is that you aren't really expected to get each layer 100% right from the get-go. The skeleton layer is your best guess, the spheres layer is your next best guess (and can deviate slightly from the skeleton), and the actual lines are your final guess, and again, can deviate from what's underneath. Each layer improves upon the last.
This being the case, having super-fine control over how hard you are pressing so that your preparatory layers do not interfere too much with the "final" sketch is of the utmost importance.
Hope this helps! Sorry if I misunderstood the question. :)