It's best to fill this in the same drawing, which makes more sense for an animation. You don't want to keep track of multiple layers. There's not many reasons for keeping them on separate layers, but if you really want to split the fills and lines, you can, using the reference fills feature.
A smart raster level has indexed colours, so each colour on screen needs its own palette entry. This means you can change the colour on screen AFTER it's been painted, which you can't do on standard raster levels. SM levels also know the difference between lines and filled areas, which helps if you want to colour or erase just lines or just fills, or apply effects to just one of them.