Those numbers are "Logical" page numbers assigned throughthe numbering and section options (and appear when you choose to view section numbering). The "Absolute" numbering of pages is not affected, and you can specify absolute page numbers inthe print dialog, but it's really just easier to change the number styling onthe section numbering options so you don't have conflicts.
Front matter is traditionally numbered using small Roman numeral, and the first part of the book corpus gets Page 1 using Arabic numerals. I generally number the cover using ABC styles if it is included in the same file.