This page will provide some tips on installing and setting up the Power commander III/usb. The instructions that Dynojet provides are pretty straight forward as far as the installation goes but leave something to be desired on simple hints for actually using the thing.
Tip #1 - The gas tank
When removing the gas tank, you will notice two rubber hoses heading to the front of the bike(on the left side of tank coming from fuel shut-off valve area). One of these has a splice and two retaining rings. If you cut the other hose, you can remove the tank much easier and splicing it back together only takes about $2 worth of parts. I can remove my tank in about 3 minutes, seat and all.
After you get the tank off, the power commander is pretty easy to install. One thing that they forget to mention in the instructions is:
Tip #2 - Power commander needs auxiliary power for it to communicate with a computer.
The pcIII gets its power when the fuel pump is getting power. This means that when you turn the key on, the pcIII will get power for that initial burst that the fuel pump puts out and then it will lose power. When you start the bike, the pcIII will have power again. This is fine for the pcIII's normal operation but for those of us who want to make adjustments with the unit still attached to the bike, it creates a bit of an issue. Try to hook the your pc up and you will notice that the power commander won't communicate with it unless the bike is running.
This is an easy fix though. Dynojet has supplied a 9v adapter for those of us who need to remove the pcIII and take it to the nearest computer. For those of you who want to hook the laptop to your bike without unhooking everything, there is a solution. After calling dynojet support, their tech informed me that it was safe to cut the 9v end of the adapter and hardwire the positive side into a "key on" circuit on the bike. Plug the other end into the pcIII and your done. (I used the wire harness to the left of the battery, which runs into the rear fender) (blue wire if I remember right)
Once you have the unit wired up, you can hook up the usb cable and turn the key on. Start the pcIII software. The software is pretty simple to use. The "get map" button will retrieve the map that the bike is currently using. The "open map file" button will allow you to import any maps that you have downloaded or saved. The "send map" button will send the map to the bike.
Now its time to take it for a spin!
If you notice some decel popping, don't worry. It only takes a few seconds to hook that computer up and make some more adjustments. (the following information is how the pcIII support tech taught me to do it) (The three buttons on the face of the unit will not adjust anything unless you put the unit in a special button mode. The reason for this is that each button changes an entire third of the map. For slight adjustments to help with decel popping and such, we only need to make small adjustments.
In the first column, you probably see 0's from 500 rpm's all the way to 7000 rpm's. This is where we are going to make our adjustments to change the air/fuel mixture.
Starting at the first column, the 2000 rpm block. You want to hold the left click on the mouse and drag it all the way to 7000 rpm's. This should highlight (turn blue) every block in the first column from 2000 rpm's to 7000 rpm's. Once these blocks are all highlighted, type in the number 10.
Every highlighted block should have changed from 0 to 10. 
After you have made the changes in the first column, you have to "send map" again. Once it reads "map sent successfully", hit save map file (just in case). Now you can unhook the computer and take the bike out for another ride.
Without a dyno, this is kind of a trial and error procedure. Start with a 10 point adjustment. If the decel popping gets worse, replace the 10's with a negative number. If changing them to 10's DID help but you still have a little popping that you would like to get rid of, start making adjustments in 5 point increments. Eventually you can work it down to 1 or 2 points. (for those of you curious, mine seems to run best at 12 with Hard Krome's 3" Black Res-Techs, but I haven't had it to the dyno shop yet).