Analogue-sequencer

Finally started making my P3 (hooray), all's going good so far and although I'm a relative 
novice to electronics construction most of the solder joints are looking clean. However, I was 
wondering about the orientation of the LED's in the function switch board. I know that the 
shorter leg of the LED is negative and notice that on the board each LED position has one 
hole "square" (by this I mean that where the metal plate shows through the green of the 
board it's etched out a square) and one hole "circle", question is which one's positive, which 
one negative? Also is this a standard way of marking the polarity on boards? Many thanks in 
advance, and apologies for lack of correct terminology,

In fairness I imagine this may well be just the start of threads by me about stuff like this as 
construction goes on!

P.