The easiest way I find for sorting out chapters is to arrange the files so that each chapter heading is at the top of a file. Then Use the Edit TOC tool, erase any existing entries, and use the Generate ToC from Files option. That will give you an NCX TOC with each file as an entry, and the beginning text of each file as the title text (Chapter 1, Chapter 2, etc., if that is what your first lines are in the files.)
To split files with the editor, use the blue split-file tool at the bottom of the preview pane.
To merge files, select two or more files in the file browser panel, and right-click. One of your choices will be to merge the files.
Sometimes, the start of a chapter will not split properly because it is buried in a paragraph or a useless <div> -- you just have to edit the code to fix that before you can do the split.
You can often find chapter heading that are not with obvious with regex searches. I've seen a lot of books with just 1, 2, 3, etc. that have no style different from the main text, and they are hard to spot. A regex search something like <p class="whatever">\d+ (or even just >\d+) will often make finding them easier.