i dont know the exact details of what affect playing someone in the wrong position or in the wrong formation has, i can tell you what it does do though, it lowers that persons chemistry.
when a persons chemistry is low, it affects their passing, i dont know if it affects anything else, but im pretty sure it affects passing.
this is an example, not real. say for instance im xabi alonso (best passer in the game) and im in the right position and formation (chemistry is 9 or 11), i will only make 1 poor pass out of 20, now lets say my chemistry is now 7, i will make 1 poor pass out of 15, now lets say my chemistry is 5, i will make 1 poor pass out of 10, chemistry 3, 1 poor pass out of 5.
obviously the worse the person is at passing the worse those stats get.
im pretty sure it doesnt affect positioning, or anything else.
this is my theory below on morale.
morale on the other hand im pretty sure affects all the players stats, lets say 99 morale is 100%, and 0 morale would be 1%. if im on 99 morale all my stats will be at their full potential, if im on 0 morale they will all be at 1% of what they should be. e.g. if im at 99 morale, and im nilmar my pace is 90, if im at 0 morale my pace is at 1 or thereabouts.
if you dont think that is true, go into single player, pick real madrid and edit all of their players down to 1 for everything, 1 for stamina, pace, passing, shooting, etc, this will take about 20 minutes to do and is very boring. now use barcelona and play against real madrid on legendary, even though all the players have 1 for pace i.e 1 acceleration and 1 sprint speed, they can still keep up with messi, even with 1 standing tackle, they can still tackle messi. obviously not as good as before but there is a slight difference. therefore it has affected the game but not as much as you think it would.
therefore morale should be kept high, it makes your players peform the way they should.
i also think that morale is random in normal matches (hidden morale) but it is skewed in favour of better players. e.g. drogba, messi, ronaldo, etc, will most of the time have high morale, whereas crap players will only have high morale sometimes, e.g. shaun wright philips.
all of the above is my theory from playing the game, its also why when you play ultimate team and then play a normal online match, it feels slower, because morale is random when playing a normal match and therefore only some people will be running at full pace. whereas in ultimate team your morale is high (if your good or use cards) and they always run at full pelt.
also why its easier to score finesse shots in ultimate team and harder in normal online, free kicks are also easier in ultimate team, this is all due to morale and it affecting all of your stats.