I'm also a fan of Scrivener.

With short stories I normally work between Scrivener and Google Docs, but I've never had to do any layout for print before.
For visual novels, I normally work in Scrivener, but then once it's transferred to the engine I might do short snippets in the engine itself. (Though I will do a once over spellcheck if I do any in engine work). From there it's fiddling with the code and the results until I'm happy with everything. It does go a little faster once I've established the feel I'm going for, like a template to compare it to.

Not much in tips or advice unfortunately.