I haven't been able to find the restart info yet, that word appears way too many times when I search here.
Can you add many books at once using the one you mentioned, KCM? That's what I like about the nook's bookshelf feature. I'm confused too since you say it's a PC app, but you actually add things to collections on the Kindle itself.
Or maybe I'm just thinking too hard, and read more into it than you actually wrote.
I don't mind trying multiple options, I'm just worried about keeping the integrity of my Calibre library. I don't want to take the slightest chance of it getting corrupted or messed up in any way.