Welcome to the very confusing world of fuel injection tuning. I have a lot of old school type friends who still struggle with some of the concepts, but I'll try to give you some overview of what it's all about.
As you may know, fuel injection is a computer driven process as compared to the mechanical process used in carburation. Instead of jets of varyious sizes that control the amount of fuel, a computer determines the amount of fuel by controlling the duration of the feed during the combustion process. Ultimately in fuel injection tuning you're trying to achieve an efficient and effective air to fuel ratio. In a well tuned bike this fuel ratio isn't constant throughout the RPM settings. It's typically leaner (less gas, more air) at lower RPM's and richer (more gas, less air) as RPM's increase. Lean settings can give you better fuel efficiency (and in a lot of cases better responsiveness) at the cost of higher temperatures with the opposite being the case with richer settings. A "map" is simply a table of values that defines how much fuel to feed for a given RPM and throttle setting.
With a fuel injection tuner you can easily change this map to suit your needs versus having to go to the dealer and have the ECU flashed. By and large injection tuning isn't about creating more overall horsepower as much as it is optimizing the power (responsiveness) for any given throttle/horsepower setting while balancing it against the heat produced by the combustion process and the mileage. Although it seems counter-intuitive, a richer setting actually makes the engine run cooler and that's why, in most maps, you'll see leaner settings at low rpm/throttle and richer settings as the rpm/throttle increases.
Those are the main concepts behind it all and the implementation of how it's done varies with different manufacturers of these injection tuners. The differences tend to be about how much precision and control you want over the tuning process. Products like Power Commander allow you to individually tweak almost every aspect while others like Cobra do it all for you automatically through some pre-determined logic, with other products allowing varying levels of control and automation.
I'd tell you more, but i can see your eyes are glazing over at this point just like some of my old school buddies...good luck..