There are different approaches... but one that I use...
Set up a raster level on the left of your xsheet and the Toonz raster and Vector levels to the right of that.
Then you can paint on underneath the Toonz raster and Vector levels.
This is also very useful because we can copy/paste from the Toonz raster and Vector levels directly into the (standard) raster level.
So you might color something in Toonz raster or Vector... but then just transfer it to the raster level.
Then think of the raster level as the color level and the other levels as (primarily) line and fx levels.
That's a basic breakdown... lots of variations to that theme.
The main takeaway is that it is easy to move from Toonz Raster and Vector to (standard raster) but not so easy the other way around.
Still we can leverage the strengths of each of the levels when we use them together.
Keep us posted on your progress!