If you're working with a traditional publisher, they'll have their own standards for paper size and margins and so forth. Don't worry about it.
If you're self-publishing, the company you work with will normally have a set of page sizes that they support. Pick one that works for you. They usually have minimum margins because of limitations of printing equipment. (If you want "bleed" -- printing very close to the edge of the paper -- this typically costs extra.)
In any case, I wouldn't worry a whole lot about things like font size and margin while you're writing. With modern word processing software, you can take care of that when you're done. An exception to this would be if you are writing a book where what lands on each page is important. Like if your book has a lot of illustrations and you want the text that goes with each illustration to be on the same page or a facing page, etc.
Besides that, the only reason to worry about page sizes and margins and such is to help you track if your book is coming out to a "reasonable" length. Like if you're writing a novel and you figure you're half done and it's only 25 pages, then maybe you need to add more material. If you're half done and it's 600 pages, maybe you need to cut things out or break it into multiple volumes. Etc.