No Ph.D. needed, just some basic understanding of what you are dealing here with.
Almost all bought books and all out of the library have a non-copy-me system on board which is called DRM. This is why you had to authorize your device with the Sony Reader Library to make it jump over the DRM hurdle and be able to read your DRM'ed books.
DRM is actually owned by Adobe and Adobes solution to make things readable is ADE. Of every book there are $0.22 royalties due to ADE.
Either you download your books with the Sony software or with ADE. When the little download window opens, it will tell you which software it is going to use to transport your book to your computer. This will make it easy for you to find it later.
Calibre is not able to handle DRM as it does not pay any royalties. It is basically your old card index box to manage your library. Now being on a computer it can do a lot more than your index cards, like convert file formats.
Now, do you remember your book had DRM? And Calibre does not handle DRM? So, what does this mean? Right, you are! You can't convert your file with calibre alone. There are third party plugins available on the internet to extend the powers of Calibre to remove the DRM, to enable Calibre to convert the liberated files. But this is not to be discussed here.
You will not need it to read your books with your device as long as you stay clear of two shops: B&N and Amazon. They have their own DRM schemes or formats. Everything else as long as you buy epub files will be readable right from the start. All you have to do is to use either ADE or the Sony software to get it onto your reader.
Now wait and see: There will be a myriad of people jump now to tell you, you can use Calibre too to make this. Which is right, but would only confuse you further.
You stick with ADE or the Sony RL and you will be fine. Actually all this is very easy. All you have to do is overcome your dislikes to handle this kind of things.
