Brilliance.Chief covers most all of it nicely.
I'll add a little. There are 2 different kinds of tuners, piggy back and flash.
Piggy back tuners trick the ecm into doing what they want, and usually work well.
Flash tuners actually inject the desired tune into the stock ECM.
Ok I lied, there are also a couple of tuners that replace your ECM with their own ECM.
For popular combinations the piggyback tuners generally work pretty good, but you won't be able to have a dyno tech fine tune every thing.
The flash tuners generally give access to all the variables in the tune, thus giving the dyno tech or you (depending on the model) the ability to tune them all. These tuners are great for odd combinations of parts or for the OCD among us.
Many of each type have "auto tune" modules that can be added. Most of these modules actively tune your bike to an AFR that you (or your dyno tech) selected. Some do more.
As I suggested in another thread I would call Fuel Moto and speak with Jamie about the combination of parts you decide on. Those guys are knowledgeable and seem to be honest.
Also if you purchase a tuner from them they give lifetime map support. You simply email them your new combination of parts and they send you a map. (Probably best to call/email first, then buy parts) also they will assist, through phone/email with any issues you have.
Bat Bob has a Dynojet Power Vision from Fuel Moto.
I do not work for Fuel Moto or get paid in any way, those guys have just been awesome to me. Besides those crazy guys live in Minnesota, too dam cold for me.
Ray, almost every word I typed I learned on this forum in the past two years. I only knew Honda and Yamaha until 2011, and those only a little. We didn't mod those. They were transportation and they were fun,but I've learned that HDs have souls or something. I'm learning as fast as I can.