Hi Yorg. Since my controller doesn't have an autotune feature (yet), I'm familiar with manually tuning PID algorithms.
A good resource is the PID entry in wikipedia. They do a good job explaining how the different parameters affect the control.
PID controller - Wikipedia, the free encyclopedia
To manually tune a PID, good data logging is a must to see how the different parameters affect the algorithm. You could start with some generic parameters, get some data, and tweak from there. The "Pid w/o a PhD" article posted earlier had some example parameters, look at Figure 18. Although each system is unique, at least this will give you a starting point. This is a fun way to really get to know your system.
The other option is to autotune it yourself. Again, this assumes that you have good data logging. The Ziegler–Nichols method, which is explained in wikipedia, is a pretty common way for controllers to autotune. Basically set I and D to zero, and increase P until you get an oscillation. Make sure it's oscillating, not settling out! Once you find that critical P, measure the frequency of the oscillation and use the formulas to calculate your new parameters.
I hope to get some more information up on our website related to PID tuning. As we get more and more data from different systems, we'll make sure post them.