My ebook readers are in different places and I use them for different things, so I have different books on them all.
* I use one mainly for when I'm eating my myself -- that one usually has some sort of cozy mystery. (Sony PRS-505; this is the one I take on vacations.)
* I have one for when I'm relaxing at home. (Kindle 3rd Gen)
* I have one for work (iPod Touch) while I'm waiting on my computer -- that one is usually something I can easily break from when my computer has finished the thing I'm waiting on.
* I also have a fourth reader (iPad) for when I'm at my kids's swim classes. I only have 15 minutes where they are all in the pool at the same time; the rest of the time, whoever is waiting for their turn or for the other classes to end plays games on it.
I don't sync any of my books since half the time, I can't, and the other half I forget it's an option.
Also, I don't read more than one book at a time on any given reader, even if it's a device with multiple reader apps, for no reason. When I had one reader, I only read one ebook at at time. (And didn't read as often or in as many places as I do now.)
Since all of the books are different types, styles, and genres, I don't have any trouble keeping the storylines straight.