I regularly (always) use two large round fenders when launching and retrieving the boat: one is hung on the cleat outside the helm window (or the opposite window, but I prefer the helm side as it is more convenient when single-handling); the other I hang near the rear of the boat.
I have found that the rear cleat is too far back, allowing the fender to be pushed behind the transom. So I wrap the rearward fender around the base of one of my downriggers, which are located near the back of the cockpit. That location works well.
At the launch, before pulling away from the dock, as I untie my lines from the dock cleats I also undo the rear fender and throw it into the transom area in front of the OBs (which is where I store these two primary fenders). Then, once underway, I pull the front fender through the helm window and stand it alongside the hull below the throttle controls (it fits there perfectly, where it is out of the way but readily available).
I also carry in the boat (stored in the cockpit beneath the transom, between the gas tanks) three more fenders for use if and when needed. One can be placed mid-ships (hung from a I cleat I added inside the cockpit just behind the bulkhead), a second hung off the rear cleat, and a third far forward hung off the bowrail.
I also "made up" a pair of fender boards, which I hang when cruising canals. I have also rigged up a way of leaving as many as four fenders in place while running, by pulling them up leaving them. (Again, this comes in handy when canalling.)
Photos are available in my album, esp. the sub-album "Other Projects."