Cleanup & coloring workflow advice

I am currently entering the cleanup portion of a “Tradigital” character animation, everything is drawn, I’m not working with rigs for this one. This is the first full animation I’ve done with ToonBoom, and I could use some advice on cleanup and coloring.
Coming from Flash, my initial instinct is to separate the body on different layers so I can work on a single part of the drawing (Say the hands) without erasing or moving another part of the drawing by accident. This would also allow me to drop the alpha of one part of the drawing so I can see what I’m working on better. Since I can’t merge layers and since the body parts are moving in front and behind each other, do y’all have any advice as to a cleanup/coloring workflow?
Do you draw everything on one layer at one time, do you break it into layers, do you “Flatten” one part of the image to work on others? What would you recommend?

In traditional way, the parts of body was separated on purpose when it is animated mostly for the checking the animation due to flipping animation paper is always an issue.
Once it is on tradigital (paperless drawing frame by frame), it is easier to check the animation, it is up to the studio to reduce the amount of inbetweening drawings mostly done by inbetweener who are responsible for the clean up keys and also inbetween drawings. This however depends on the workflow that each studio is different.
To focus on clean up and for the paint for tradigital animation, you can either clean up on rough on top of same drawing or create another layer and then use light table to trace the rough to clean up on new drawing layer. If you are tracing on same rough drawing, first draw a rough with alpha channel on one of the color pot for rough (ex, blue with alpha 150). And then trace on top with black line. Once done, use ‘select by color’ (or Control + Shift + A) will let you select all the drawing currently drawn by currently selected color (on your case, you have to select blue rough color pot to select all the rough). And then delete so that only clean up line is remain. Or some use second method by creating a new layer for the clean up to keep the rough but however ends up having more layers in the scene as drawback. In traditional studios converted to tradigital, they are working on the second method since the layout, key and inbetween animators are separated so they are using script which is provided on Animate Pro 3 if you are using that version. If you are one man working, it is up to you.
No flatten would be often used since it is easier to move and change in rough drawings. But if you are using brush tool, make sure not to put contour smoothing to 0 (at least 1 or higher) since this creates a lots of control points that makes the rough drawing heavy.
Once it is cleaned up, you can either paint it on cleaned up drawing or you can create a color art by pressing ‘color art from line art’ icon from tool bar menu or select tool properties. And then paint it on color art. This would be benefit if you have a texture line so that the color has to be under the texture line or if you want apply the effects for the line and color separately.
I hope this helps.