Re: #1 - You can't.
This comes up a lot. Per the link in WorldWalker's sig, please this thread for explanation.
https://www.mobileread.com/forums/showthread.php?t=85232
That said, I'm fairly confident that the majority of users who had a structure laid out on their own and then converted to Calibre are extremely happy they did so. Calibre works so well and the use of Tags for organization is awesome.