If you run the EotG can you still use it, or does it count as a shooting attack since it goes off in the shooting phase?
You mean the cosmic engine? That's an ability that happens to trigger in the shooting phase. Yes, you can.
I have a question link to this topic. Can we unleash hell with the EotG ? I think it's no because it's an aptitude but if yes it could bé awesome
Well, you could... but you are going to shoot with only 8 meteoric javelins. the cosmic engine is an ability.