I am of the opinion that the suspension including tire pressure on your trailer should be responsible ride quality, and that the bunks should be used for securing and supporting your kayak on that trailer. If you need to use the bunks to augment the suspension of the trailer, then you might want to look at adjusting that suspension.
I worked very hard on increasing the weight, adjusting the leaf springs (removing 2 of 3) and finding the best tire pressure based on recommendations and trailer weight. After doing that, my trailer rides like a dream. I have over 1500 miles on it in the last 30 days. My kayak is strapped well to the frame, resting on the bunks with some lateral support provided by Rhino-Rack Saddles. I also store my kayak on my trailer, but loosen or remove the straps during storage. All trailer will bounce given the right - or wrong - conditions - but overall my setup works incredibly well - for me.
Dr.SteelHeads trailer was DESIGNED for the lighter loads of kayaks, my Harbor Freight trailer was designed to carry much heavier loads and required a lot of work and experimentation to get to the point I am today. I am hoping that the lessons I learned can be used by others right from the start. (But if you want to spend less time screwing with your trailer and more time fishing...go DR's route! I on the other hand really did enjoy the heck out of this build and learned a LOT more about trailers than I EVER wanted to know.)
Here is a picture of my trailer prior to adding a ladder rack and cargo basket (added the rack and cargo rack both to add weight and allow me to carry a second or third kayak).

Here it is with the ladder rack and cargo basket installed.
