Calibre is a *conversion* tool, but not an editor. when creating an ebook from zero, i recommend you use sigil, which is an epub editor (it has its own forum here) and which will allow you to define your css (div and p spacing), your TOC (toc editor), add anchors (directly edit the html code...) etc. you can also find a lot of information about creating epubs in the epub forum. and please don't hesitate to ask if you have any questions.
and since i see you are rather new, welcome to the forum ! there is lots of great info here and plenty of friendly, helpful people !