Good practice is to go into Training Mode, choose "Free Kick Training" or whatever it's called and place the ball in the area. It turns into a penalty then.
It works like this:
1) The length of time you press on the shoot button, the higher your player will kick it. Too long it'll spaz over the bar, tap it and it will be a shot along the floor. There really is a VERY FINE line between hitting the roof of the net or just skying it, but with practice you can get the feel for it just right
NOTE: Whilst holding the shoot button DON'T hold any direction AT ALL...
2) Your guy will then start his run up. DON'T hold ANY direction until your striker is about 1 step away from kicking the ball, Not Before! Again the length of time you hold it down decides how far to one side you'll kick it. And again, like the shoot button there is a VERY FINE LINE between hitting the inside corner of the net or it going miles wide. But once you do it a few times, it'll start to feel natural i promise!
3) Some players are better than others at taking pens too. This does affect whoever is taking the penalty at the time. You can check your player cards to see if there are any players with a "Penalty Taker" one assigned, this should help more also.
4) If you are playing on PS3(?) i would also suggest switching from analogue stick control to the D-Pad for penalties too as it seems to be easier to judge how long you have held the direction down for. With the analogue stick it feels too loose but with the D-Pad i personally feel more control over the penalty.
Hope this helps!