" If you jack your car up at the specified jacking location, where do you put the jack stands?"
I start by lifting from the rear jacking point, which will raise the front enough to get a jack stand in there. Then I do the same thing on the other side. Once the front is raised I lift the entire rear by lifting from the suspension mounting point and put both rear stands in place.
Do a forum search - you'll find a few different methods people use and then pick the one you like best. Also, there's a write-up in Pelican's technical section which describes another way to do this. Look here:
Pelican Technical Article: Jacking Up and Lifting the Boxster on Jack Stands - 986 / 987