The Private Use Area can be used any way that you wish, but with OpenType glyphs there’s no need to map them at all — just insert new glyphs.
FontCreator’s Complete Composites and Glyph Transform features use a lot of PUA code-points for quickly generating Petite Capitals, Superscripts for Ordinals, Discretionary Ligatures, etc. If you select the PUA code-points that you have used, and then Complete Composites, you may find that they are replaced with other glyphs. If they are not mapped, that cannot happen.
See the Complete Composites tutorial for details.