There are three stages to creating a symbol in Eagle - the PCB footprint, the symbol and the final part which includes connections.
You can put the pins anywhere when you draw the symbol. Usually you assign unique names to each of the pins. When you create the part you select a PCB footprint and then define the connections. That stage is where the pins are identified as being in the correct place on the footprint.
There is probably a tutorial for it in the manual or help files.
Keith
P.s. There is a good help forum for Eagle on Cadsoft's site