If you want to start page numbering on page, say, 3 of a document, you have to stop Indesign reshuffling all your pages and ruining your layout (your first page will now be a double page spread). So first you have to:
Select all pages (click on the first page, hold down shift, click on the last page), then:
Page window tab menu > deselect “Allow document pages to shuffle” and “Allow selected spreads to shuffle”.
Then you change the page numbering by selecting the page (3, for example) that you want numbering to start in the page window and go to:
Page window tab menu > Numbering and section options > Tick the box for “Start section” > Start page numbering at > 1
Now in the Page window your page numbers will look like: 1, 2, 1, 2, 3…….