When sending magazines and books to print, should the cover and the content pages be in the dsame file, with the cover being the first pages, or the cover need to be submitted in a separate file for printing?
How does the printer know which pages are the cover?
There's no NEED to have it as a seperate file, no. I would, however, create sections in your document so that the cover pages are in a different numbering scheme, and your inside pages can start as page 1 on a new section. e.g. Cover (i, ii), Inside pages (1...whatever), Back Cover (iii,iv). Keeping it together is especiallly useful if you are creating a PDF of the whole document for other purposes. Just instruct your printer which pages are the cover. It's likley obvious to any printer these days, but you should always discuss the project otherwise. As mentioned, you'd be good to consider a separate file especially if the printing process, stock or binding is different. I personally go back and forth depending on the project.