Book manager – Mac + iPad

I've been an Apple user for some years, but I never managed to find a good book manager.
As by now, I use a quite uncomfortable routine in order to read books (I should mention that most of the books I read are PDFs, I read a lot of open source books on computer science):

• I download them on my Mac
• I add them to iTunes, and I edit their properties by, for example, taking advantage of the composer field to store informations about the publishing house and the genre field to store the "topic" of the book (which is awful, I can't group books based on these details, just based on author/category)
• I sync all of my books with my iPad, and I read them only from there (using iBooks), because I don't like the fact that on my Mac I haven't got a version of iBooks (what I need is a system that remembers the last read page, for instance)

What I'm searching for is an iTunes-like book manager that provides me with a desktop version which lets me organize my books properly (for example adding multiple authors, tags, categories, publishing house), sync them with my iPad (with last-read-page syncing at least) and read them in a proper way.
What I mean with proper way is that while both iBooks and Kindle app let me switch from white to sepia to black background on eBooks, they won't let me do that on PDFs. I know that changing text size in PDFs is quite an hard task, but I don't think changing the color is too.

If someone is wondering, I already tried Papers 2, but it's most suited for academic papers than for books (in my opinion). If nothing comes out from this question, maybe I'll try to stick with Papers for a while.