UP2 board CPLD misbehaving

OK, i managed to throw out a 1Hz blinking led by writing my own code and i understand it fully, but the original problem of other LED's flashing on the board is still occuring. I've only specified one output pin in my code, yet the neighbour pins are also being toggled it seems.

Is this simply a result of the Fitter + Router using logic elements that are nearby physically, and because i'm not using the pins it is ok to "mess" with them? If i were to use those pins, would it re-route the noisy parts to other parts of the CLPD?

Also, i'm still not quite sure what the different pin icons of the Pin planner represent. Is there a reference chart or a primer somewhere so that i can read up on this?