I've got a burning question that my friend and I have tried to find a solution too, we've tried a number of ways but alas none have worked. We could use your help.

We want a specific unit to be damaged when inside of a transport ship, here's the kicker. Each player has between 3-7 units that need this effect and there are an estimated 40 possible transport ships available to them.

Ill make an example; P1 William Wallace, once garrisoned inside anyone of his teams available transport ships (20 on average) William Wallace takes 20 damage every 15 seconds until he is dead.

Thanks in advance for your help, and a prompt reply would be greatly appreciated.

Help us, you scums!

Damage only Hero class?

The trouble is there are more than just the 3-7 heroes for each player, but only the select few heroes must be damaged, and only when inside transport ships.

Watch your language.

That is in no way profanity, so slow your roll Ryuu before i hit you with a Hadoken.

Is this for Beren, Luthien and Earendil?

This is for Nhoobish' METW victory conditions, but yea the exact same idea as with luth ber and earn

Stick heroes in a ship to prevent heroes not being assassinated as there isn't a warship spawn? I can't help because I know nothing about triggers but I've always thought in principle, killing a particular unit as a victory trigger is a silly idea Open to abuse, not worth the trouble

Condition: Units garrisoned works only with numbers....else Bring Object to Object makes too many triggers, probably Object Target doesn't work too
Effect: like this(i damaged only archers of the eyes)

Thats a valid point, but its the whole basis of Hanni, I guess the fact with Hanni atleast is the people playing know not to do that.

Damage object trigger only at water area? Did that worked?

I think the flaw with this trigger Coat is that even if the unit inside the Transport isnt an Archer of Eyes he will still become damaged. Because you cant set the unit type in the Condition : Units Garrisoned.

Condition : Units Garrisoned - Set transport as Object - set 1 as value
Effect : Damage Objects - Archer of Eyes - 5Hp

or just kill them all

No it didn't. The reason being that when the unit is inside the Transport Ship, the unit isn't actually on the water area, the Transport Ship is.