There are basically 2 methods of doing this.
The cut-and-splice method, where the hull of the jet ski is cut away, including the engine and pump, and that is bolted into the bottom of the boat as one piece.
The fabricated aluminum method, which means fabricating mounts for the engine and welding into the hull. Also, fabricating your jet unit tunnel where the jet unit will bolt up. Most PWC's have the intake duct as part of the glass hull, only a few have a bolt-in duct, so, you will have to use one of those. However, Kevin Turner, one of the members here, recently posted about some aftermarket intake ducts for yamaha pumps, which appear to be a lot better than the thin OEM ducts.
Now, as far as the rest of the boat goes, the design possibilities are endless.