It's best that you do the shield BEFORE the sword when going from Animus to Novus. Apparently they screwed up and you can't get alexandrite from FATEs if you upgrade your sword first.

As for atma to animus, you can do either one at any time you wish. Most people go for the shield first, since it only requires 2 books to do. But I did the sword first because I wanted to get the harder part out of the way.