To clarify how calibre talks to iTunes and your iPad:
When calibre starts up, it looks for connected devices that it knows about. If it finds one (whose driver is enabled), it will ask the device driver to return a list of the books on the device.
Because the iPad driver works through iTunes, the process is less direct. Calibre asks iTunes to return a list of books in the iPad 'Books' playlist for display in the Reader window. As described in the
first post in the 'Start here' thread, the first time that calibre connects to your iPad, this process takes longer than subsequent connections. If you have a lot of books on your iPad, this could take a few moments. At this point, calibre has only read information from iTunes.
In your scenario, you have books in iTunes that you've added on your own. No problem there; calibre will display those in the Reader window. I'm guessing that the books you've added to iTunes are the same books you have in calibre.
Let's say that you have lots of books added to iTunes, and just a few books on your iPad. Forget about calibre for a moment. How books are transferred from iTunes to your iPad depends upon your iTunes sync settings. The relevant settings are:
- iTunes|Preferences|Devices Prevent iPods, iPhones and iPads from syncing automatically. I have this checked.
- DEVICES|Summary|Options Sync only checked songs and videos. I have this checked.
- DEVICES|Summary|Options|Manually manage music and videos. I have this checked.
- DEVICES|Books|Sync Books. I have this unchecked.
Depending upon how you have these options set (and perhaps others), the behavior of iTunes can be very different. It's possible that some combination of settings is causing a sync operation which transfers books from your iTunes Library to your iPad Books playlist.
You can test this theory by restoring the original conditions with a few books on your iPad and (I'm guessing) lots of books in iTunes. Without calibre running, try syncing your iPad. If it's sending your entire book collection from iTunes, then there's something different about your sync settings that's causing the behavior you're seeing.
Now, back to calibre. Unless you click the 'Send to device' button, it is not possible for the driver to upload books to iTunes, because the driver has no knowledge of the database - it can only deal with books passed to it when the user initiates an action. My guess is that because your books in iTunes happen to be the very same books in calibre, you're seeing a sync operation between iTunes and your iPad and mistaking it for calibre uploading books.
You stated in your initial message that you would rather manage your iPad books independently of calibre. No problem - just disable the iPad driver in
Preferences|Plugins|Device Interface plugins.
If you're trying to help this community, then we need to better understand how your setup is different than others here. If we can pin down the differences, I'll add that information to the 'Start here' thread.
G