You should think of the master page as including any information that you need for any and all pages of a single format. This would include headers/footers and the layout of the text on a page (for instance the margins, or number of columns on a page).
Once the changes to a master page are made, they may need to be applied to the appropriate Body pages in your document. You should only explicitly change a body page if you know that the change is only for that page, and that any changes to the document are not going to require those changes be undone.
In the Body pages you should only include the body of the document. Any text, figures, tables, etc. that you may need to include would be inserted here. Since these are generally not duplicated, there is no need to place the information on a master page.
For more specifics on changing margins, including headers and footers, etc., see the other Frame stock answers.