I don't create them with CutePDF; I create them with Acrobat Pro. Which, of course, is not freely available. I think there are freeware bookmark tools available, but I'm not sure what they are, and I'm certain they're not as smooth & simple as using Acrobat's conversion process.
But I suspect anyone who wants PDF ebooks for 6" screens, is going to want them custom formatted--if they didn't care about bold & italic, or choice of fonts & pt sizes, just wanted page splits and bookmarks per chapter, they can use LRF, Mobi or Epub files, depending on their reader.
I'm not sure who falls in the niche of wanting ebooks in PDF format, with no choice of fonts, pt size, or margins, and no ability to include text formatting or pictures. The point of PDF is that it has all those features; for plain text with just the chapters marked, the other formats do much better.
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