There is some confusion regarding chapters and pages. The EPUB standard uses the term chapters to define how ebook content is organized, since EPUB was initially designed for reflowable content. Once EPUB introduced fixed-layout, it continued to use chapters to refer to the individual pages of an ebook. Since Kotobee Author's project file is based on the EPUB format, likewise the term chapters is used. This is merely a term and can be used to represent pages.
When creating large chapters, depending on the reader being used (either Kotobee Reader, or an external ebook reader) the chapter may be either displayed with a vertical scrollbar, or divided into fixed number of pages with the ability to navigate horizontally. Kotobee Reader uses a vertical scrollbar to navigate through long chapters. It is recommended to organize content as much as possible into chapters and subchapters for ease of navigation.
When importing a PDF document, you will find that each page of the PDF is automatically converted into a chapter. That is entirely fine. What needs to be done, is to hide the inner chapters such that they do not appear in the table of contents. That is done by setting the Invisible property of these chapters. Then the only chapters that will appear in the table of contents are the chapter beginnings.
To have a better understanding of the differences between chapters and pages, this is an important read: https://www.kotobee.com/blog/epub-navigation-peculiarities/