If 2 players have very strong chemistry which increases the overall chemistry rating for the team but will the chemistry only be effective for the 2 players concerned or do all connections just contribute to the overall chemistry which affects the team evenly?
The chemistry between 2 players directly affects those 2 players - that is certain. But at the same time it adds to your team chemistry which affects the entire team.
As a general rule you should try to have a line between all players and try to get a high team chemistry, rather then only a few thick green lines and lower team chemistry.
But this is the answer your are really after...
EA do not fully explain the exact math behind how team or 'connection' chemistry affects a team or players. As you can imagine if they did it would spoil the game dramatically as everyone would end up playing with the exact same 'awesome' team. It would take the 'fun' out of it.