You may implement PD4PageMark.getHtmlTemplate(int) method, to return different footer definitions depending on a page number. See the last code sample on
PD4PageMark.setInitialPageNumber(-2) should (in theory) set page number 1 to the third page.
There is no way to reset page numbering. But you may generate two PDF documents with independent page numbering and to merge them. As far as I remember your PD4ML version supports PD4ML.merge()