If you run into the cafe you lose 20 points. If you destroy X-ATM092 (which you can only do on the bridge) you'll get a 100 point bonus. The best way to beat it is to have Quezacotl's compatibility at 1000 and have SumMag+10%, 20%, and 30% and boost abilities (it has 5500-6500 HP). If you beat it 8 times you can get 400 AP!!! You'll lose some SeeD rank points, but who cares since you can raise it so easily?

Other things affecting SeeD rank:
1. Talking to people. 1 point deduction per conversation
2. Going to the comm. tower before Seifer tells you to. 1 point deduction for each attempt.
3. Jumping off the cliff as a shortcut. 5 point deduction
4. Not saving the dog during your escape. 10 point deduction.
There are other things that affect it too like time remaining, enemies defeated, times escaped, etc.

Btw, this info is from my handy dandy strategy guide.