(This is going to be long but I hope you will find my experience helpful.)
You really want to think about what your goals are for doing the tuner thing to your bike. For example, are you going to drag race the bike, are you just going to ride it around town, are you going to tour with it, etc. Many guys are do it yourselfers but if you are like me with a new $26K 2011 RGU and don't want to F it up, you are going to pay someone to do the job. A honest and competent tech ought to give you a recommendation, based on your goals, about what type of tuner to use, whether to use canned maps, dyno the bike or not and if so, how much dyno time to meet your goals. Bottom line, however, is that you will always get the best out of your tuner and bike if you take the time (and spend the cash) to dyno it. If you are going to drag race your bike and you want to get evey single ounce of power out of it you would want to dyno it up to 100% RPMs. You must be aware, however, that putting that much stress on the engine and tranny while on a dyno does have the possibility of engine damage or overheating and blueing the exhaust pipes, etc. If you are just into touring, for example, you might only want to dyno it to 80%. This reduces dyno time and therefore cost. In this scenario a good tech can give you a very acceptable download for the remaining 20%. Anyway, lots of things to think about before getting started and if the guys that are going to do the job for you can't talk to you about this kind of stuff then you need to find someone who knows WTF they are doing.
After lots of discussion with a couple of HD Dealers, their service managers, and the techs who would do the job, I settled on one particular shop. The tech, BTW, who I insisted had to do the work, had done somewhere north of 500 dynos. This particular shop, after lots of experience with tuners over a number of years, carried both the latest version of the SE tuner (because they had to as a HD Dealer) and the TTS Mastertune. I won't bore you with the details but the owner of TTS Mastertune developed the SE tuner for HD and left the company after some kind of falling out and started his own company. You can check this out on the internet. No question that both tuners will get the job done but the TTS has more sophisticated software that allows the tech to more accurately and quickly tune the bike. I was fortunate enough to be allowed into the dyno room with tech and watched the whole procedure. The tech showed me both the TTS and SE software and why they preferred TTS which was clear to me after the tutorial on both products.
When I bought my bike new, I put SE Stage 1 and Reinharts on it before I drove it out of the dealership so I never really rode it around in a completely stock situation except for the demo ride. At the time, they downloaded the standard HD Stage 1 map which I'm sure continued to make the bike run lean and added some minor level of HP and Torque to the stock set up. My bike ran fine but there was some exhaust popping and such due to the lean condition. Ultimately, my goal was to give the bike more juice for touring (passing power, etc.). Based on the tech's recommendation, I elected to go for the the TTS Mastertune which cost slightly less than the SE tuner. I had them dyno it to 80%. Once completed the TTS was disconnected, my map was downloaded to a thumb drive. I keep both the tuner and the thumb drive in one of the saddlebags just in case. Final numbers were an increase of 10+hp and 10+ ft. lbs. of torque to the rear wheel. What a difference! The additonal power was amazing. The bike jumps at the crack of the throttle and there is no exhaust popping. Just got back from a 3,400 mile trip. It was fun to blow around tractor/trailers with authority on the interstate in 6th gear by just hitting the gas.
Whew! My fingers hurt from typing. Time for a couple of brewskis. Ride safe gang.