I just bought the Windows version 1.8.6.0 and after setting up a file in the binder and wanting a footer in my printed file when I compiled the text file I found the compile functions do not work in the page settings fields. I spend a few hours going through several permutations and found that the text file needs to be under Manuscript, Chapters and the best I could do is get a Word 97 file out then use Word to put in the header/footer I wanted. This compile function does not work very well at the moment. I don’t know how to proceed to send relevant info to designers to fix this. As an aside, I think the preview print function should work to see what the post compile did.
The Draft folder (renamed “Manuscript” in your template, identifiable by its special icon) it the special folder in Scrivener intended for compile; it holds only text files and is the default compile group. For the most part, any files you want to be part of your compiled document should be housed in the Draft folder.
The header and footer is set in the Page Settings of compile for the formats that support it–this includes RTF, DOC, and DOCX. Section 23.13.1 of the user manual deals with adding the header and footer in compile.
If you can be more specific about your settings and what you’re trying to accomplish, we may be able to offer more help to get the compile working as you want. If you haven’t taken the time yet to go through the interactive tutorial (available from the Help menu or from the Getting Started section of the New Project window), I suggest looking at that as well; it may help make some unique aspects of Scrivener clearer, and there’s a section that walks through a few compiles to give you a feel for that.