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1. As the name implies, the second tab is used to specify how to save books to disk, outside the Calibre Library, the third is used to specify how to send books to the device. Depending on how you navigate among the files on your device, you may wish to use some special structure. On disk you may have other needs.
When you add books to the Calibre Library, neither of the two last tabs are relevant. Just the first.
2. The regexp-string you use to add a book, and read information from the filename, must match the acual filename. So if the file has the author first in the filename, then the regexp must also read that first. In your save template you save the authors name before the title, but in the regexp used to read the filename you try to read the title first in the filename. Note that directory names are not used when reading information from the filename.
Also if there happens to be "-" in the title or in the author name, then the regexp will be fooled. Try to match the spaces as well as the "-" to make the regexp harder to fool.
3. Yes. But only if you don't use a separator between the empty elements. This is the reason why it is good to have different templates for saving to disk and for sending to device.
When you send your files to the device unused parts will become an empty string. So if a book doesn't belong to a series, {series} and {series_index} will not be written. But if you have {series} - {series_index} then the "-" will be added to the filename. So don't use a "-" between parts that may be empty, when sending to the device.
When you send to disk and you are going to read back the information from the filename, that can be a problem. So don't. This is no problem for me, since I am happy to keep my books in the Calibre Library, along with the metadata. And only send to my device now and then.
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