If arriving by metro there is one entrance and if arriving by electric train there is another entrance. Both entrances are connected by an underground passage.
This is necessary as there are two different kinds of trains converging here both with differing gauge track.
If you take the electric train from Piraeus, Omonia or Kiffissia for example you will debouch right in the square from the building below left.
If, however, you take the Metro from Syntagma square you will either have to walk the underground passage to debouch in the square or exit directly onto Athinas Street and walk 1/2 a block to the square.
This may be important for you to know if you have luggage to carry or when meeting friends.
So differentiate when telling your friends where you will meet.
Simplest thing to do is just meet by the church unless its raining which it never does in summer.