Sebastian,
These all connect through the 25x2 header on the GPIO board, which is labelled with the circuit (on the right) and the processor port/pin (on the left). For example, an adjacent pair might be PA0/VB2 meaning that if you jumper those pins, CPU port AD pin 0 will be connected to circuit VB2, which in turn is connected to Ampseal pin 12.
The CPU has six I/O ports with a total of 25 pins. The ports are AD (analog-digital converters) , T (timer ports), M and S (communications), E and A. In the code and documentation, these are called PAD0
x, PT
x, PM
x, PE
x, and PA
x, where
x is generally a number between 0 and 7. All of these ports can be used as general purpose I/O as well (some with limitations, though).
However, the point of having the 25x2 header is that you can move the circuit to any pin with a jumper, if you need to do this to suit your application.
You can find out much more by studying the schematics here:
http://www.msgpio.com/manuals/gpiohw.htm
Lance.
"Never wrestle with pigs. You both get dirty and the pig likes it." - George Bernard Shaw