Pandoc is a magical piece of software. It'll handle anything you give it, and with just a few bits of tweaking, you can get its output to look like anything you want. It can turn your work into a book-formatted PDF with page numbers, anchors, a table of contents, and anything else you might need. And by changing a few arguments, you can have it generate an epub in whatever style you like, complete with autogenerated metadata.
As writers, it's always best to write in whatever environment you're most comfortable with, and pandoc won't interfere with that in any way. Be it Google Docs, Microsoft Word, Libreoffice Writer, or just a plain text editor, pandoc will take it and turn it into anything you want.