How can I install a timer with three-way switches?
If you have more than two screws on a switch it's probably a 3 way. The other option would be a 120v/240v switch or something like that for a motor load possibly. If you have a black screw where the red wire is tied to on each switch, it's a 3 way. Yours are probably both 3 ways. They would not operate if they weren't. Anyway here are a few variations on how to wire that up:

http://www.wfu.edu/~matthews/courses/p230/switches/3way/variations.html

great and easy to follow!

Forgot to mention the timer has to be a 3 way timer as well. From the pdf you linked it didn't look like it was unless I missed something. I know a lot of those are both single or 3 way depending on how you want to use it.