I believe the only thing the arrows do is moving their centre of influence. Putting up arrows on attacking midfielders make them matched with the opponent's defenders instead of central midfielders.

Likewise, putting down arrows on your defenders makes them marking the opponent's STs more tightly but makes it more open to midfield runs and long shots.

If you use zonal marking, the arrows and the positions of the players make great impact to the game, if done incorrectly you may have a critical flaw laying on your formation that leave you open to attacks (a backfield flaw) or counterattacks (a frontfield flaw). Usually, a high scoring result was caused by these flaws which could be eliminated with proper player selection and placements.

If man-to-man marking is used, the arrows don't make much difference.