With raster-based programs like PDN this is really the only way to go.
My personal workflow involves lots of cutting, pasting and merging layers on a per-glyph basis. Anything that demands to be shaped a certain way, you're best off setting your own guidelines with the line & shape tools. Doing stuff like this, it's generally a solid plan to work in as large of a base resolution as your machine can handle, that way you'll reduce AA artifacts and the overall generation loss that comes inherently with rotating rasters a bunch of times over. apy's "AA's Assistant" is an amazing plugin to cover your tracks in that department!