Once your rod holders are mounted, that will, determine the length of rod you can best carry in them. For instance, my rod holders and the space I have works best for 8'6" rods - they're mounted on the exterior of the sliding windows (I think Rapala brand, holds 4 on each side). 9' will fit but they start to poke out too far into the access to the cockpit from the dock behind the cabin. They still fit, but I risk a clumsy or unknowing guest snapping off a tip. Shorter than 8'6" and they bend and flex too much in the middle. For the fishing I do, 8'6" is a great length. For the more stout halibut rods which are 6' or 6'5" etc., I carry them standing up in another location.
If you're mounting them inside the cabin, along the roof, consider placing them close enough together to handle 2 piece rods broken down. These might also handle the 6 ft. rods.
For the rod holders used while trolling off of the stern, I like rail mounted Scottys, NOT Fish Ons which are too whimpy.
One thing that concerns me was this comment from above "the ceiling to sag a bit under the weight of the poles". Seriously, from the weight of fishing poles? I just presumed the C-Dory ceilings were strong enough to walk or crawl on. Are they or aren't they strong enough to support a large human? Do they bend or sag if you crawl on them? Stand? CW