I take it you have “Use export formatting” checked in Text Options in the Export Draft sheet. If that is checked, the formatting you have defined in the Export Draft sheet be used, which, of course, means that if you have left-justified text as your export formatting, that will override any centered text. Either uncheck the option in Export Draft, or check “Preserve Formatting” for the individual document.
I don’t understand the question. Footnotes can be exported either as footnotes or as endnotes. So saying “footnotes and end-notes act the same” has no meaning in Scrivener. Scrivener only has footnotes, which you can choose to export as end-notes if you want. And this only has any meaning when exporting to RTF and you open it in a word processor that reads footnotes (Word, Mellel, Nisus). For other formats, footnotes just get plonked at the end of the document. I’m pretty sure this is covered in the tutorial and in the FAQ.
Please remember that Scrivener is not a word processor. This is made explicit in numerous places - in the tutorial, in the readme file, on the forum, in the FAQ. Do not expect Scrivener to do extensive formatting. It can export a document with basic formatting, but if you need more advanced formatting, as you obviously do, you need to export your draft and open it in a word processor for final formatting and tweaking. This is why it is called “Export Draft” and not “Export Manuscript”.
Also, could you please tell me if the answer I gave you in the following thread helped you?
literatureandlatte.com/forum … .php?t=625
If you post a problem it helps if you let me know if my answer resolved the issue, so that I know there isn’t a bug here. Thanks.