The text in my headers is showing up like a ghost behind the text of my chapters. I just got a Mac, so imported my novel from Scrivener for Windows. I’m not sure if this plays into the problem. I’ve been over and over my compile settings and the document settings. My margins are the same as they were in the Windows version for the 5.5x8.5 print book.
Please help! 
In the Page Settings compile pane, you’ll find the header and footer settings in a grid. You might not see anything here based on what you are describing, as it sounds like you might have some carriage returns in these fields pushing the content down into the page. Maybe try copying and pasting out to an editor and then just replacing them with the placeholder code or text you want.
It took forever for me to get back to this. Sorry. I took a look and didn’t see any way to find out if there were extra carriage returns. So I chose the regular novel format and compiled it really quick. The problem is gone. I figure it must have had to do with bringing the file in from the Windows version. Now I just need to set all my compile preferences again. ugh. Oh, well. The Mac version is 100 times better, so it will be worth it. 
And I’ll get some practice. Thanks for your reply.
Maybe not! Most of your compile settings (stuff in the Meta-Data pane and Contents are project specific) can be saved into presets, which you can then apply to other projects in the future. Use the “Format As” menu, and at the bottom you’ll find a command for managing them. Use the old project to save the settings, and now you should see that entry in the other project’s “Format As” menu.