Calibre would most likely replace some of the software on your PC. Nothing on the e-reader.
Calibre would make it easy to get books from many different sources and in many different formats, since you can easily rename, convert and rearrange as you please, using calibre.
I don't use Evernote, and don't have a Sony e-reader, so I don't know if calibre will change anything regarding how you use Evernote with the e-reader. I suspect not.
If you still are curious, why not test it? Calibre is free to download and use.
There is a separate forum for Sony e-reader owners. You could perhaps get better answers there? Perhaps there even already are some answers there for you?
https://www.mobileread.com/forums/forumdisplay.php?f=100
Also I tried to Google "Evernote calibre" and there seems to be many Evernote users that also like and use calibre along with Evernote. It seems that there even is a forum at Evernote, that could also be a good place to ask about how to use calibre with Evernote?