The following is how I did it using Pages '09 v4.3. I assume you have a later version of Pages, but the concepts are the same.
You might want to duplicate your document and practice with it before altering the
original.
Note: “Use previous headers & footers” in my version of Pages is the same as “Match previous section” in later versions of Pages.
1) It would be helpful to click View > Page Thumbnails and click View > Show Invisibles.
2) On the Document tab of the Document inspector, select Headers and select Footers. You might need to adjust the top and bottom margins.
3) Assuming your document is contained in one section, click anywhere in your document and deselect (uncheck)
“Use previous headers & footers” on the Section tab of the Layout inspector. Thus, every page in your document will have
“Use previous headers & footers” deselected.
4) Break your document’s pages into sections so that the first page of each chapter will be in its own section and the
following pages of each chapter will be in their own section: Starting with the
first chapter, put the insertion point at the end of the first page of each chapter and click Insert > Section Break, and put the insertion point at the end of the last page of each chapter and click Insert > Section Break. You
might not need to insert a section break at the end of the last page of the last chapter.
5) Working with one chapter first-page at a time, click in the footer on the first page of each chapter (it doesn’t matter which chapter you start with) and then click Insert > Page Number. The proper sequential number will appear in the
footer on that page. Keep going until all the chapter first-page footers have numbers.
6) Working with one chapter second page at a time, click in the header on the
second page of each chapter (it doesn’t matter which chapter you start with) and
then click Insert > Page Number. The proper sequential number will appear in all
the headers of the following pages in that chapter.