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I really like Mantano. There was a year or so during which it was pretty unstable while they fiddled with features, but it's almost as stable as Aldiko now. The big feature that has sold me on it is the nestable collections (so instead of just "cookbooks", I can have "cookbooks/vegetarian", "cookbooks/Italian", etc.).
I used Calibre Companion for a while and almost liked it. The first reason that I didn't like it is that it's copy-protected, so I couldn't put it on my devices that don't have Google Play (I have several). Second, wireless transfers are slower than USB, so I ended up not using them. Thjrd, after importing the books I use Mantano's interface rather than Calibre Companion's anyway, which eliminates one of the big reasons to use Calibre Companion.
Instead, I keep a "Calibre" folder on my memory card and use Calibre's "sync to folder". It works just about like Calibre Companion, but without the wireless. The downside is that I haven't figured out a way to convert Calibre's tags into Mantano's collections, so after importing them into Mantano, I have to arrange the books into my collections myself.
The problem with the NOOK app is that it doesn't register itself to Android as opening epubs, so you can't open books in the NOOK app using Calibre Companion's interface. Additionally, the NOOK app expects sideloaded books to be in a particular folder and don't recall being able to change the folder that CC saves books to. You could, though, use calibre to sync straight to your "My Content" folder (or whatever NOOK calls it; I don't remember off the top of my head). Both of these statements are from memory, though. The Calibre Companion guys claim to be generous with refunds, so it can't hurt to try and see if you can make it work how you want.
I guess the short of what I'm saying is that I use Calibre and Mantano in just about the same way that you propose and, though it isn't perfect, it's better than any other system I've found.
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