So is there any difference between the two? Does one do something the other doesn't?
Henry,
Really, it's just two different ways to get to the same place. The biggest difference, other than the reputation of the respective manufacturers, is that the SE 6-speed has a true overdrive ratio in 6th while the Baker DD6 is direct drive in 6th (1:1). Direct drive is more efficient in transferring power, and quieter as well. The final drive ratio's of both products is the same, since the Baker changes the primary gear ratio to achieve the "overdrive" affect, so the road speed vs rpm is the same.
Getting back to the original post of this thread, if the reason for changing the gearbox is to achieve a lower first gear for trailer towing without increasing top gear rpm, I would suggest the SE 6-speed, or better yet the original Baker 6-speed (OD6), coupled with a smaller compensator sprocket (24 tooth vs 25 stock). Just order the wide ratio version of the gear set, which has the lowest first gear ratio (3.24 I think). Give the folks at Baker a call, let them know what you are trying to accomplish, and they'll offer up their suggestion.
Jerry