Just make the book how you want it. Then the very last thing to do before publication is to edit the OPF file outside of Sigil and remove the incorrect "cover" reference item from the guide section. 7-Zip will allow you to edit the file without even unzipping the archive. You just need to remember that if you ever open it with Sigil in the future, you'll have to edit the OPF file again. It's fairly painless to make it part of your workflow. I do it all the time (removing various guide items like "cover") when I'm preparing an epub for conversion to mobi with Kindlegen.
I
do wish it (Sigil) wouldn't automatically tag that first xhtml file as the guide section cover reference (regardless of what it may contain). I'd much prefer that marking an image as "cover" would simply create the meta-tag entry and leave it completely up to the user to decide whether or not that first xhtml page is to be marked as the cover reference in the guide section. The handling of a cover image is vague enough in the ePub specs to make it reasonable that the user might need to be the final arbiter of exactly how it's dealt with. But I'm not sweating it too much, since I've learned how to work around it.
