Okay, I try to make it short and clear. If I fail to do so, I will gladly expand on these matters.
1) Counter attacks are covered on p. 71/72 of the rulebook. If you declare a counter-attack with a unit (must be declared before the attacker rolls dice), the unit and thus every model of the unit is passively activated. You choose the melee attack type, spend the action tokens and roll to hit.
Important: Counter attacks can only target models/units which attacked the unit before in melee. So not just the models that got attacked can make counter attacks, but all models of an attacked unit, as long as they can make valid attacks against models who attacked their unit before.
You can make one counter-attack against each attack. That means you can counter-attack several times as long as you have action tokens left, but only once against every attack.
Same goes for individual models. To stay with your example: If a unit of three models makes an attack action against a single model, this model can declare and make one counter-attack action. If the unit attacks again, the individual model can make a second counter-attack.
So if an individual model has 5 ACT and a 2 ACT-attack and gets attacked by the 3 models, it can spend 2 ACT and make an attack, but not 4 ACT to make two counter-attacks at once. However, if they attack again, it can spend another 2 ACT to counter-attack again.
Of course, if a model has a special rule that allows several attacks as part of the same attack action (like ambidextrous fighter), it could choose to make such an attack as its one counter attack action.
2) You normally need a line of sight to attack models in your melee range. Bases of other models block LOS. So you normally cannot attack over bases, even over the bases of your own unit members. Same goes for the attacker. So you could basically protect models within a unit by hiding them in the last rank (although that would hinder them from attacking as well).
The Hoplites rank fighting allows to ignore this rule for the bases of their own unit members.