The traditional way of managing ebooks is by creating a hierarchy of directories by topic. If there is a book that is goes across topics, you either create a shortcut or copy the file over. Managing this can become a nightmare. After some time, we may have duplicates, and we do not know where they exist, as the file names could be different. If we are synchronising with e-book readers, you need some way of knowing which books are in which reader. We may also need to know if we have books by a certain author but catering to different subjects. It would be best if each file had tags associated with it. We may also want to have the book cover and other meta data associated with it.
I use a software called Calibre and its creator has come up with a portable variation. I can install this portable variation in my external hard disk and I become independent of my computer, as nothing has to be installed on the computer. Which means, I can plug my hard-disk to any machine and use my ebook management software.
Calibre also has plug-ins which allow you to search for duplicates. It can use different libraries and switch between them. You can also create your own columns for better database management. It can connect to a variety of readers and smartphones via USB. It also has news readers inbuilt into it.
Full disclosure: I do not get any revenue out of recommending this. This is free, and if you like it, you can donate. I do donate each year a certain amount.