Numbering - Input XML Fragments
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The numbering affects three parts of your publication, the table of contents, headers/footers, and chapter titles:

The Table of Contents

The table of contents is a tree of <topicref> elements. 

<map xmlns:ditaarch="http://dita.oasis-open.org/architecture/2005/" ...>
    <oxy:front-page xmlns:oxy="http://www.oxygenxml.com/extensions/author">
        ...
    </oxy:front-page>
    <opentopic:map xmlns:opentopic="http://www.idiominc.com/opentopic">
        <title class="- topic/title ">Publication Title</title>

        <topicref is-chapter="true" class="- map/topicref " ... >
            <topicmeta class="- map/topicmeta " ... >
                <navtitle href="#unique_1" class="- topic/navtitle ">Overview</navtitle>
                ...
            </topicmeta>
            <topicref class="- map/topicref " ...>
                <topicmeta class="- map/topicmeta " data-topic-id="dcpp_resources">
                    <navtitle href="#unique_2" class="- topic/navtitle ">Resources</navtitle>
                    ...
                </topicmeta>
            </topicref>
        ...
    </opentopic:map>
...
</map>
Note: The <opentopic:map> element contains the effective table of contents structure.
Note: The TOC items are the elements with the class: - map / topicref.
Note: The ones identified as chapters have the @is-chapter attribute set.

The Header and Footers

These are based on string sets generated for the titles. The complete set of strings is defined in: [INSTALLATION_DIR]/css/print/p-pages-and-headers.css.

The CSS rules that build the string sets are matching the map title from the front page and the titles from the content.
<oxy:front-page xmlns:oxy="http://www.oxygenxml.com/extensions/author">
        <oxy:front-page-title>
            <title class="- topic/title ">Publication Title</title>
        </oxy:front-page-title>
</oxy:front-page>
The main content is organized as follows:
<map xmlns:ditaarch="http://dita.oasis-open.org/architecture/2005/" ...>
    ...
    <opentopic:map xmlns:opentopic="http://www.idiominc.com/opentopic">
      ...
    </opentopic:map>

    <topic is-chapter="true" oid="dcpp_overview">
        <title class="- topic/title ">Overview</title>
        <body class="- topic/body ">
            ...
        </body>
        <topic class="- topic/topic " id="unique_2" oid="dcpp_resources">
            <title class="- topic/title ">Resources</title>
            ...
        </topic>
        <topic class="- topic/topic " id="unique_2" oid="dcpp_parameters">
            <title class="- topic/title ">Parameters</title>
            ...
        </topic>
    </topic>
Note: The topic content comes after the <opentopic:map> element.
Note: The child topics are the elements that have the class - topic/topic included in the parents.
Note: The ones identified as chapters have the @is-chapter attribute set.

The Titles of Chapters

The titles from the content are children of the topics:
<topic class="- topic/topic " id="unique_2" oid="dcpp_parameters">
        <title class="- topic/title ">Parameters</title>
            ...
</topic>
Note: The title elements have the class: - topic/title. The actual element name can be different.