I'd suggest you get some coaching, and commit to a few sessions. Not knowing exactly what is going on based on what you describe, here are some general tips that might prove fruitful:
• General rule of thumb is be aware of the water, but don't fixate one particular wave. Tip: Instead try to get in sync with the rhythm of the water (it's constant, despite appearances).
• For most paddlers, the first thing to go when they feel threatened is the foot pressure on the footboard (and as a result that, your bum also loose contact with the back of the cockpit) that will diminish your connection to the ski and the water around you. Tip: When you feel threatened or unstable, keep the foot pressure on!
• The best brace is a good catch: Ski's are incredibly responsive, and will do whatever you tell them to; good bad or ugly. Tip: Develop a good vocabulary of skills that help your ski listen to you, chief amongst them is a powerful catch and stroke that will allow you to stay connected to the water and make balance adjustments dynamically.
• New paddlers tend to struggle with too many moving parts, moving in the wrong direction and at the wrong times. For example, your paddle has enough purchase to pull you in the water if used incorrectly. Tip: Limit the liability of your stroke by simplifying the movements you make. Focus turning your entire body into a lever that moves at one point, and one point only (your hips). A handy way to experiment with this is to pretend that you have no elbows, and that your hips and shoulders are locked together like two hinges on a door (they must rotate together, not one faster than the other).
• When you get into dynamic water of any sort, the tendency is to "juggle". This begs for mistakes to be made, because no one can juggle water. Tip: Slow the game down, and focus on the fundamentals. To build better balance and technique, try paddling in slow motion, in figure 8's in progressively more dynamic water. This will force you to not juggle, but instead focus on maintaining your connection to the surfski and the water around you.
There are other tips, but I suggest you get Dawid Mocke's book "Surfski with the Pros" to cover the good stuff. Also, Epic has a nice technique series that should be helpful for covering the basics.
www.epickayaks.com/article/article/epic-technique-series