Welcome.
One app you can look at for organization of books is Calibre Companion. You can easily browse your books on a shelf or list with various sorts, but also view them grouped by author, series, tags, etc. and once you find the book you want to read it can be set up to either open the book in whatever you set as the default reader or you can get a list of apps you have installed that are compatible with that format and pick which one to open your book with.
https://www.mobileread.com/forums/sho...d.php?t=188899
https://www.mobileread.com/forums/sho...d.php?t=219822
For reading apps (of the non-store type) take a look at Moon+, Mantano, Aldiko, Cool Reader for a few of the more popular (But, there are tons of reader apps to choose from). For me personally I find I use Moon+ Pro and the Kindle app the most and occasionally use the Kobo app and Mantano.