Drawing
Ink, paint and palettes
Ink a drawing once and paint it as often as you like, recolor a whole show from one palette, and shade it with soft tones and lights that stay inside the lines.
Line and color art
Keep a drawing's clean lines on one layer and its paint on the layer under it, so painting never disturbs a line and lines can be redrawn without losing the paint. Pick the layer with the drawing and choose Insert > Color Art Layer: its fills move to a new layer under it, named after it with Color, and the strokes stay where they are.
On the color art layer, the Paint Bucket fills the regions the line layer's strokes close around where you click, even where the color layer has nothing yet, so you can ink first and paint after. The paint lands on the color layer and the lines stay untouched above it. Both are ordinary layers in the saved file.
Two more ways to paint quickly: the Paint Bucket's Fill all regions fills, with one click, every enclosed area of a shape that has the same fill as the one you click, and a brush in Repaint mode recolors the fills it passes over without painting anything new on empty areas. See Paint Bucket and Ink Bottle and Brush modes.
Linked palettes
Open Window > Palettes. A palette is a set of named colors (skin, hair, outline, shadow). Add... makes a named color from the current fill color. Select art and choose Fill or Stroke to color it with the palette color and link it; Link Matching links every fill, stroke and text in the document that already has that color, which is the quick way to bring existing art into a palette. The number beside each color is how many uses are linked to it. Unlink takes the links off the selection, and Remove takes a color out of every palette; what used it keeps its color.
Edit... (or double-click a color) changes it everywhere it is linked, as one undo step. From the ... menu beside the palette list, New Palette... makes a copy of the palette in use under a new name, such as Night: recolor its colors, and switching palettes in the list recolors the whole document. The same menu renames and deletes palettes. The colors are written into the art itself, so the file shows its last coloring anywhere it opens; the palettes and links are kept with the document for Phoenix.
Sharing a palette between documents
A show's characters keep their colors from scene to scene when every scene's document links to the same palette file. From the ... menu, Save Palette to File... writes the palette in use to a .phxpal file and links it; in each other document, Link Palette File... brings that file in (taking the place of a palette of the same name) and recolors what is linked to its colors. The panel shows the file a shared palette comes from.
Changes go both ways. Editing, adding or removing a color in a shared palette writes the file at once. When a document opens, and whenever you work in the Palettes panel, Phoenix reads the files again: what another document changed comes in as one undo step, recoloring the art. Update Linked Palettes does the same on demand. Keep the palette file beside the documents (in the same folder or one near it), since the link is kept relative to the document, and the documents and the palette can move together. Unlink Palette File keeps the colors as the document's own. Each document still holds the colors in its art, so it opens the same where the palette file is missing.
Tone, highlight and glow
Pick the layer to shade and choose Insert > Effect Layer: Tone, Highlight or Glow. An effect layer appears above it; draw the shape of the shadow or light on it with any tool. Phoenix softens the shape, colors it and composites it over the layer under it: a tone is multiplied, darkening what is beneath; a highlight is screened, lightening it; a glow is added. A tone or highlight is kept within the layer's art, so a shadow drawn roughly over a character never spills off it; a glow spreads outside.
Right-click the effect layer and choose Effect Settings... to change its kind, color, softness, strength and whether it is kept within the layer. While you draw on it, its shape shows faintly so you can see what you draw. Effects render on the stage and in everything Phoenix exports. In the saved FLA an effect layer is a guide layer, so other apps leave it out rather than drawing its shape flat.