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InDesign follows a millennium-old tradition: even numbers on the left; odd numbers on the right. See the Pages panel menu button > Numbering and Section Options.
If you want to make 2 pages in a left-right spread sit side-by-side; make the left page numbered as an even number; for example 2.
Consider downloading my pre-made docs that show how to make gatefolds and printer's imposition pages:
If you really insist on doing it against Western-culture book-making tradition, go to the pages panel menu button, and switch off both switches that mention Shuffling. Then, you can number your pages in the non-standard way you are trying to achieve.
Perhaps I just don't understand how InDesign deals with the covers for your books... are you supposed to do them separately from the actual book? And then merge them later?
Depends on the job. If it requires different paper or is full color with the rest black only then yes, a second file would be the way to go.
Best thing to do is talk to your printer. We’d just be guessing.
I'm basically making a PDF that people can print out if they buy it. So I guess, if I get down to it, I don't even care what the page numbers do as long as they do it consistently. It just bugs the perfectionist in me that it is so difficult to figure out.
The view of a PDF's pages depends on the PDF viewer not InDesign. You can save an initial view for a facing page document in AcrobatPro and AcrobatPro or Reader will honor the view, but most other PDF readers will not. In the end you have little control over how the client sees the PDF. As long as you export Pages (not Spreads), the view won't affect the PDF printing
The initial view saved as Two-Up Continuous (Cover Page) in AcrobatPro