I was in your same boat until I took the Altera Timing Analysis training last week. Now I understand Timequest and realize it is easier to use and much, much more powerful than the classic timing analyzer.
Do yourself a favor and go take the training. It is just a different way of doing things and you will quickly realize it is also better. Altera's problem (in general, not just for this) is that their documentation is not the best. You could try the online training, I haven't taken it but it might help.
http://www.altera.com/education/training/courses/odsw1115 (
http://www.altera.com/education/training/courses/odsw1115)