Once you've applied your page size and the correct margins you'll need to think about what information you want to include in the running heads and feet of your book. The running heads and feet are little snippets of text – usually navigational aids, though they can be other things – that appear outside of the main block of text, at the tops and bottoms of pages.
The most obvious component that you're likely to want to include is the page number. Other elements that are often included are the book title, part title, chapter title, and author name.
Of course, you can't include all these items, so the design for every book will vary, depending on what elements are considered to be most useful to the reader.
Novels generally make the lightest use of these elements, often including only page numbers. These can appear at the top or the bottom of the page, and can be centred or aligned to the outside margin of each page (you wouldn't expect to find page numbers aligned to the inside margin of the pages, as this would mean that each page would have to be opened fully to reveal the page number, while numbers at the outside margin can be flicked through easily with the book hardly open at all).
Don't forget that if you align the page numbers to the outside margin this means that numbers on odd pages (rectos) should be on the right, and the numbers on the even pages (versos) will be on the left. If they are all on the same side then you've got a problem!
Many novels do include other elements as well, such as author name and book title on alternating pages, but this is really up to your own personal preferences. Try looking at different book designs and get a feel for what other designers are doing, and what approach you think would suit your book best.
Nonfiction books will normally have running heads to help readers navigate the book. Since nonfiction books are often dipped into by readers for relevant information when it is needed, rather than read from cover to cover, like novels, it's more important for readers to be able to navigate quickly round the book. Nonfiction books will often have the part title and chapter title on alternating pages, though this depends on exactly how the book is structured. You will need to consider the structure of your book and then decide what heading levels should appear at the tops of the pages in order to best assist your readers.
In terms of design, you can lay out the running heads and feet however you want. Centre align is common, as is outside margin, but (as ever) inside margin is uncommon due to its relative inaccessibility to the reader. Some running heads use small caps; some use lines to divide them from the text, while others just use blank space – the choice is really up to you, and again the best thing to do is to look at some other similar books and get a feel for the different designs being used, and which you might want to use employ on your own book.
Once you have chosen what information to include, and how to lay it out, the important thing is to make sure that you apply this consistently throughout. There aren't many right and wrong answers when it comes to page layout, but internal consistency is the one you really do have to stick to. You also need to remember that the running heads and running feet must not appear within your margins – there can be no printed material within that space!
There are also certain pages where running heads should not appear: these include pages such as the title page, half title page, and pages that start new sections, such as chapters or tables of contents, etc.