Looking at your profile, you are towing a 2008 Kodiak 25QS TT. For towing purposes you could go long bed or short bed. I don't think it will matter very much. What you need to ask yourself is, what other uses will you have for your truck?
Myself, I do a lot of "armature" home remodeling and construction (my own house and property). Been doing this type of stuff all my life. I'm always remodeling or building something, so for me, the bed of the truck is VERY important, that I can lay down a 4x8 sheet of plywood without having to tilt it, or even worse, a 4x8 sheet of drywall, so it won't be on it's side, it lays down flat.
I also have a 10 foot by 6 foot utility trailer for hauling 10 foot or longer materials and they lay down flat. Also, I take care of my mother's yard, so it's absolutely vital I have a trailer that will comfortably move a John Deer 730 series mower-tractor and in the winter with the attached snow blower.
When camping, the long bed is great because all the extras fit with no problem. Firewood, dump tote, air compressor, hoses, sewer hoses, step ladder for the roof to clean off the slide roofs before retracting. I have a 7 foot ladder, it lays flat in the back of the truck. Short bed, ladder would be too small for me to be useful to fit the bed. Extra water jugs, extra lumber for leveling the camper (2x12x6 foot boards), and a bunch of other stuff.
I'm currently now, in the process of harvesting a tree in the middle of a corn field for firewood. The 4 wheel drive, 6 wheels, pulling the utility trailer across a harvested field is priceless, especially when the ground is soft and the trailer is full of firewood.
So you see, as far as towing your trailer, either long or short will work perfectly fine. But you REALLY need to ask yourself, what else will you use your truck for outside of towing and camping.
If you REALLY want my opinion, get the long bed. You can NEVER have too much space or truck!