Hmmm, I just leave Calibre running on my linux box and attach my reader briefly in the morning to sync the scheduled downloaded news for reading on the way to work. Works for me. Of course I never turn the damn thing off
Other than that, yes, it looks like you will be running commandline. Look at
ebook-convert (linked to the recipe section of the manual) and ebook-device which is
undocumented as of yet but will yield info when executed from the commandline.