I use Aldiko 99% of the time. I use the stars to rate a book after I read it and that also tells me if I have read it or not. These stars in Aldiko do not seem to be the same ones from calibre by the way.
For sorting into series etc Aldiko does not have easy way to do this. SO I discovered FBreader can sort by series, etc. If I point it to the same folder Aldiko uses then I can use FBreader to sort books on my reader easily. I use it as a reference and still read the book in Aldiko. I only use FBreader if I am away from the computer, traveling etc., and can't use calibre.
I do not use FBreader to read because I like the Aldiko color choices better. I prefer the Autocad color scheme - dark blue background and white text.
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