I have never heard of using wax. It would be a good idea to wax the paint where the hardtop seal touches the car, but I wouldn't put wax on the rubber.
For the hardtop rubber/seals use Gummi Pflege, around $8 on Amazon. It is the absolute best thing you can put on seals and rubber to keep them from getting worn out, and it actually helps make the rubber a bit fuller, which helps avoid squeaks. I coat all the seals I can find 1-2 times a year with it.
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1999 Ocean Blue Metallic Boxster - blueboxster.com
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