RoManuV, you've probably finished your project and shipped it off by now, but I thought I'd add a couple of comments to the info coreenm provided.
When I prepare a cover file for a perfect-bound book, I ask the printer to provide the spine width based on the paper's PPI (pages per inch) value. It's usually some lengthy fraction, like .6875″ (11/16″). The way I build my template is as a single page that's (page trim width x 2) + (the spine width) wide by (page trim height) high. So, for example a 5.5″ x 8.5″ book might have a cover layout of 11.6875″ x 8.5″. The tip I want to pass on is to use ID's column guides feature to create your spine area. Go to Margins and Columns…, say you want 2 columns, and use the spine width as the gutter (in this example, .6875″). That will create perfect front cover, back cover, and spine areas for. Be sure to include a .125″ bleed all around the outside edge of your cover.
When ID5 came out featuring multiple page sizes in a single document, one of the sample docs I saw was a book cover with separate pages for front, back, and spine; but I've never known a printer who wanted a cover submitted as three separate pages.
Also, in my experience there's no problem printing the inside covers of a paperback (perfect-bound) book. You just have to pay for it. I usually submit these as a separate two-page file, one page per inside cover, at the trim size of the book (I don't worry about the spine for inside covers).