In the old days, a specialist artist would "ink" the outlines from onion skin drawings onto an animation cell.  After this was painstakingly completed, the cell was flipped over and paint was applied to the back.  This process preserved the ink outlines, because they were on the front of the cell, and the outlines generally covered up any small errors made while inking.

Later, xerographic processes were used to transfer the drawings directly onto the cells.  This sped up the process by eliminating the tracing step, however, the final product was only as good as the original drawings.

When we scan in an image, we can pretty much proceed to the Ink and Paint step if we want to.  However, there are some things we can do that will make our lives easier...

"Expand dynamic range" will compensate for light drawings, and bring out a nice dark outline for us to work with.  It also lets us see a lot of our searching lines that we want to get rid of.  If you have an animation loaded in, then it will give you the option of applying to every frame.  When doing this, the same value that was used on the first frame will be used for every frame to avoid flickering.

Careful use of the Adjust/Value or Level filters will let us get rid of unwanted lines and grain.  Once we have found settings that work well, then they can be applied to every frame with the value filter in the animation timeline.  It's almost like being able to automatically cleanup your drawings.  Still, the cleaner you make your final drawings, the easier it will be to ink and paint.  It's a trade-off on how much time you want to spend on either one.  There is also a line cleanup tool that will help you get rid of unwanted marks, but it should be used carefully.

If you did your rough drawings in non-photo blue before doing a final cleanup in lead, then there are a number of ways to remove the blue drawings and leave only the cleanup.  Using the color key filter with a blank swap image would be one way.  You can also use the Non-photo blue removal tool.

The flood fill tool is used to fill in areas of drawings.  Use the Tolerance setting to determine how much the paint 'chews' into the outline.  The cleaner the outline is, the easier filling will be, so be sure to follow the steps above whenever possible.

Using the Anti-aliased option will make your fill a little smoother around the edges, and will chew into the outline a little softer.  Filling over and over with this option will make your fill expand outward -- very useful for getting those hard to reach places.  You can always restore the edges later, so why not take advantage of it.

If you really want to preserve those outlines that you worked so hard on throughout your drawing process, you can switch to the 'multiply' fill mode on the fill/gradient panel.  This mode will keep any part of your image from being erased by a fill, so you can chew in as much as you like.  Beware though, that filling a second time over the same color will darken your image.  If you're working on a single image, the little bit of extra time you spend can really pay off using this technique.

There are many ways to proceed with ink and paint, so instead of telling you what the best way is, and expecting you to follow like a drone, we'll simply suggest some tactics that can be worthwhile in saving some time.  Ink and paint can easily become one of the most time-consuming parts of your animation, so it's worth deciding for yourself where to spend your time best.

Don't worry if you 'chew' into your outlines.  There are a number of ways your can restore them later - after all you painting is done.  Just like the ink and painters of the old days, who preserved they outlines by painting on the opposite side of the cells, you can preserve your outlines for later use by saving a copy of them and combining them back in later.

The timeline has a composite with sequence option, for example, that will let you overlay your original line drawings back over the painted version.  It's a good idea to save a copy of the original line drawings separate from your painted ones for such an occasion.

Here, the outline was added back by picking it up as a custom brush and pasting it back on top.

The broken line -- oh my!

If you have a broken line in your outline you may spill a lot of paint.  It's a simple thing to fix on-the-fly, though.

It's a good idea when doing ink and paint work to know your keyboard shortcuts.  They'll save you an awful lot of time.  You can use the 'd' key to switch to draw mode and fill in the little broken line.  Don't bother switching colors to the edge color.  It's just a little dab your going to put down, and nobody will notice.  Once you've done that, you can switch back to the fill tool with the 'f' key.

Bare in mind, some controls and windows can swallow keyboard events, so you may have to click on the main window to get it back.

Instead of switching colors several dozens times for every frame in order to fill every part of a character, consider painting with only one color at a time, advancing though the entire animation.  Then proceed to the next color...

Save your colors that your use in a well.  This will let you load them in later when working on a different animation.