In email tracking, is the click rate a % of all recipients, or a % of only those who opened the email? Also, if I have the same link twice (one at top and one at bottom) does it track which link is...

The opened % and clicked % are both calculated against the total number of emails sent. So if you sent to 100 people and 70 opened, and 20 people clicked you get a 70% open rate and 20% click rate.

Regarding having the same link inserted multiple times in your email, it counts as the same link. However you can track it if you add an anchor #something at the end of it.

For example:

Link at the top of your email:
http://mylink.com#top

And your link at the bottom
http://mylink.com#bottom

You can write anything after the # , whatever helps you identify the link placement.