Everything you would ever want to know about this can be found here:
Jacking the Boxster
If it is the seam in the first picture, that is a safe place to jack the car from. The jack stands should be placed under the four actual jack points. I would not want the car resting on anything other that those points for an extended period of time. Nothing should be bending, and if it is you should stop and double check everything is correct.
Some people like to use a hockey puck, adapter, or rubber guards to avoid scraping the anti-corrision coating off of the car. I don't think it is really an issue unless you do it enough to substantially wear down the coating.