Make sure that there is not water under the driver's seat and it there is clean it up ASAP. (Immobilizer/Central locking unit is there)
A few places to look for leaks:
The drip trays around the engine compartment get torn, or the drain hole becomes clogged. Recently a few people have posted about repairing and replacing them.
The drains in front of the windshield on either side of the batter become clogged. That area can fill with water causing damage and leaks into the car.
Door seals... Make sure the windows are operating correctly. 986 windows are a little complex and the regulators usually begin to fail when they are 15-20 years old.
The window seals should keep water out if they are intact, but if water gets into the door it can leak inside the car if the plastic (foam) door liner is compromised.
Tech articles here related to the body should be helpful:
https://www.pelicanparts.com/boxster/boxster_tech.htm
Last possibility: AC condenser drain. Not sure if it's a problem on the 986s, but have seen it in a Cayenne.
Covers: I keep my cars outside most of the time and have gone through a lot of covers. How much do you want to spend?
A nice "Porsche" brand outdoor cover is probably best.
Next: ($250-500) Custom fit covers with Noah or Weathershield HD material worked well for me and looked good for over two years before they started to deteriorate.
Cheap: I bought some ~$50 custom fit "all weather" covers. They fell apart in less than a year and let dust and water through.
Right now I am trying "
Duck Covers Weather Defender Car Covers" size 170"x60"x48". Not a custom fit, but close enough for the money. For around $50 I'm happy with them. They are 'water resistant' and look like they will hold up well for about a year.