The plastic panels that are under the Boxster take a beating and those on my 2000 S are no exception. I had pulled the 3 rearmost panels off for an engine swap so I spent some time fixing them.
I do the repairs using fiberglass, which is not perfect because it does not bond that well with the Boxster's plastic, but I have worked with it in the past and it is what I have on hand. It does seem to do the job.
The small panel that covers the fuel and power steering lines under the left side door just had a couple of holes in it so was easy, (before the repairs).
... as was the middle panel, just some cracks down its center so it was straight forward to reinforce the affected areas.
The rearmost panel, that goes from one side to the other, was more of a challenge. All of the mounting points were either missing or broken. I used thin aluminum to approximate the necessary shapes then fiberglassed them on both sides. Pop rivets were then added to strengthen the bond between the fiberglass and the plastic and to hold it in place in case of delamination.
With a coat of black paint the panels are far from lovely but should be functional.