Not sure if anyone else has had this experience, but I opened/imported/updated my dissertation (in progress) in version 3 and all the margins were reset when it opened for the first time. I can open the backup file in 2 and see that the margins are where I set them in the original.
Perhaps I'm doing it wrong, but I like to see how it will look in the final document, so I try to keep everything looking just as it should after compiling. If anyone has tips on the best way approach this, in case I'm missing something, I'd love to hear them. The way I've done this in version 2 is just by setting them manually, as I've never found a universal margins setting anywhere.
As with most dissertations, all my pages need to be double-spaced (mostly), Times New Roman or similar, and for margins: "A margin of 3.8 cm (1.5 inches) on the left-hand side of the pages is required to allow for binding. Minimum margins of 3 cm (1.25 inches) are required at the top and the bottom. A 2.5 cm (1 inch) margin is required on the right-hand side."
EDIT: I realize now that I had used the page setup margin settings to set the old document margins, and that those weren't preserved in the move to version 3.