The spaces between paragraphs are missing and things I’ve centered are not centered in the epub.
I want to make sure I’m not messing up somehow. I started with the basic format then added the cover and metajunk.
Is there something else I’m missing?
This is probably all just due to the e-book compile bugs Lee is fixing for 1.0, but just to be clear, when you say “spaces between paragraphs” do you mean empty lines in the editor or between-paragraph spacing? They both have bugs anyway–empty lines are being stripped when they shouldn’t be, and between-paragraph spacing is being taken from the editor–formatting in general (to the extent that ebooks allow it) is being taken from the editor, rather than from the compile settings, so that also might be why you’re not getting that. Alignment issue is again a bug that’s been fixed for 1.0.
Yes.
I write this:
[b]The Bestest Manuel Ever
by Me[/b]
and it comes out
The Bestest Manuel Ever
by Me
Which of course for that part is okay in the content there is no spaces between the paragraphs.
Sorry to hear it is a bug, but happy to hear it wasn’t something I had messed up. 
Ah, okay, yes, that’s been fixed for 1.0.