If you're using the download option attached to a print project, then definitely don't do anything different (especially exporting pages as "facing pages", or spreads) from your what you have to do for your print project as the files also need to comply with the print requirements (and definitely don't include a "cover" image with your interior file).
If you're creating a separate project using the ebook project and uploading a PDF as your "interior" file, again you don't need to use the "facing pages" option as PDF readers like Adobe Reader or Digital Editions have the option to open the file in "book" style.
Yes, you do need to use the "cover creator" step as that is what puts a cover image on your storefront, but yes you can also put your front cover image as the first page of your PDF and the back cover image as your last page in your PDF. If you're inserting a jpeg as the "cover" and the first page of your PDF, you can also upload that at the "cover creator" step for the cover image on your storefront. That's what I've done for my ebook.
