I used to read online books so it's comfortable to keep all of them in my phone. But I also used to organise all info wich I got while reading to use it for papers writing (college essays etc.) like I did few days ago with help of https://paidpaper.net/ and I did it well.. I have used quotes and some usefull chapters from last book I've read and it helped me a lot.
I don't really think about it too hard. I try to keep the books from the same series together and in order, that's about it. I also try to keep an even distribution of book sizes next to each other, as well, I suppose.