I have both. 26' boat is kept on a trailer and stored outside during summer. I use the full cover whenever its on the trailer and parked. I use the cockpit cover when parked in the marina, when trailering during rain, or if its only out of the water for a day or so. Trailering takes its toll on the cockpit cover but it beats road grime all over the interior.
The full cover is a ***** to handle alone but less work cleaning and rewaxing. My gell still looks good for 10 years old.