My skimmer basket is a couple inches below the decking. I cut out the decking above the basket and add two pieces of wood to the bottom of that decking to hold it together and maintain proper spacing.

I then screw in support pieces underneath the deck to support the wood I cut out.

See the pics below and it will make more sense. I've had a couple of decks and always solved the skimmer issue this way. Kids will run across the skimmer and this method ensures that there wont be any accidents. It looks good too.