One problem solver I discovered is shortening your cast. Speeding up your tempo on casts will also help. It will keep line speed up in the air and not flailing behind or in front of you. Often when I go to trade shows I can tell who fly-fishes in saltwater versus fresh water by the style of casting the angler has. Trout fisherman usually cast straight over the head while flats-fishermen cast more to the side.
Line management is also an important thing to consider.
Often I take out a client that wants to try and fly fish from a kayak. One solution, as mentioned earlier, is to shorten your cast. The towel will keep you from getting your line hung on gear and rigging on your vessel. If the towel won't stay put, dip it in the water and it will surely grip. You might also try stripping your line out of the vessel and into the water.