Tell us about yourself!
From the ARM CPU point of view those signals are GPIOs (General Purpose Input/Output), the Pn.nn designation is the original ARM signal names on the chip itself, so you can know exactly which ARM pin you are using. In the smoothieware design they are all assigned to a specific function but it's only a name written on the board and within the config file. The config file design is enough flexible to allow you to use them as general purpose as well so to redefine their assignment. It's an advanced feature for people who knows what they're doing. It's a very smart design and I personally like it more than adruinos based boards.