Firstly i'd like to say hello. i'm a noob and this is my first post. However i own all 3 pes games and play many matches every day. I've just included a note on FK's as having read this thread there seems to be some confusion about them:
The main difference between holding up/down and R1/R2 is that up/down influences the overall trajectory of the ball whereas R1/R2 effectively influences the trajectory after the ball has passed the wall.
R1 has the effect of "keeping the ball up". By that i mean rather than dipping the ball, the ball has a flatter trajectory after passing the wall and stays in the air longer. Basically it is the opposite of dipping the shot. It is not overly usefull except when hitting v.short fk's(if u don't have a becks or rivaldo on your team). Try aiming at the GK's near post, holding up on the d pad,giving 1/2 power and holding r1. Often these shots hit the post or underside of the bar and go in. At worst the GK will block the ball down, possibly to your waiting player.
R2 however is extremely useful. Basically it "dips" the ball, and if used can make the diff between a goal and another good effort. Personally i use it when taking every FK because it allows me to apply more power to the shot without it going over.
Also, one last thing, i got the impression that some people use R1/R2 by holding them when taking the free kick. In my experience this does nothing. Try pressing it just after letting go of the shoot button and hold it for the duration of the FK.
Hope this helps. if i've confused anyone tell me and i'll try to explain a bit better.