I do. I have a scupper pro. In short:
I attach a small grapnel anchor on a line winder (buy from all good spearfishing stores) and clip this to the front so I can leave the yak where I am diving, on about 12 metres of light rope.
I use the standard rear well for my dive bag, clipping it in.
I attached a large dive flag (buy a large flag at least A3 size and attach it to a standard kayak flag base).
I have some stretchy bungy lines clipped to some extra rings I attached to the top of the hull, and I clip my spear under some of those when travelling (always connect to float line as well in case it falls out).
I put my dry bag in the front hatch with clothes, first aid kit, headlamp, duct tape, handheld VHF, cellphone. I also have a waterproof case for my iphone which I use.
You need a paddle leash, and a bungy line that holds the paddle secure when yo are not on the boat.
I bought a kayak sail which is choice for fun but certainly not essential.
Benefits are it is a much nicer way to get out diving, peaceful out on the waves or in the early morning gliding over the shallows watching the fish and stngrays beneath you etc ... you don't need a mate to help launch a boat, you can launch almost anywhere, most dive spots are within easy kayak range but a long swim from shore, low running costs, you don't need a grunty tow car, you will enjoy the paddling for paddling's sake and for fitness, also you can take plenty of gear like lunch and drinks and even a tent and sleeping gear if you want.
Need I go on?