Yeah, Ywriter5 seems pretty good. I tried it, but went back to Scrivener, maybe because I'm just used to it. But it does a lot of the same sorts of things. Also, I can use the free beta of Scrivener in Linux, and I'm not sure Ywriter has a Linux version.
I used to use Scrivener, but now I write in Createspace format in Libre Office so I can fix hyphenation as I write. Then I have scripts to convert the Libre Office file into a .epub that I can upload to e-book sites so I only need one source file to produce files for all of them. Converting into manuscript format should just be a matter of changing a handful of styles, but I haven't tried that yet.
Ywriter5 doesn't have a linux version, but I believe it is very WINE compatible. I probably wouldn't even go to the trouble if I were in your shoes, though.
I've been doing mine in Google docs. It may not be as great as Scrivner or some of the other programs out there but the $0 price tag definitely fits my budget. After each chapter is done, I Ctrl + C the whole thing and paste it into a Wordpad file on my desktop. For each piece I've written there is a main file folder, and inside is a separate file for each chapter along with any notes and research pertaining to the project, brainstorming, flow charts, character bio's, etc... and one long save for the entire work in one long document.
I go for manuscript style, however I don't write anything all that long. I would imagine a larger story would be a pain to work through as such.
I think it's just personal preference. My first draft is all one manuscript, then I save each chapter separately as I edit it, then it gets added into a second manuscript (which I keep a hard copy of).
