Missile Silo Tutorial
Properly used, the Missile Silo can be detrimental to even the most extreme fortifications. It is not cheap, so it should only be used when everything else fails.
Damage can be dealt to single structures or over large areas. The Eos does 3500 damage with a small blast radius, aim for points where multiple buildings touch to apply this damage to more than one building. If there are bigger clusters of structures, the Inferno can be used as it has a much bigger area of effect.
Shields and Terraform
Every missile except the Shockley will be stopped by full shields. If the shields are slightly below full charge, the Eos can pass through them as well. Shields can be circumvented by either stunning or weakening them before firing the remaining missiles. For a successful stun, first scout all aegis and then use Shockleys to stun them, keep the small AOE of the Shockley in mind. Multiple stuns might be needed to deactivate all shields if they are spread out. Alternatively, an Eos can be used to weaken all shields in a shield network. After firing one Eos, any following Eos will pass freely through the shields, as long as the shield get a few seconds to equalize their charges.
Terraform can be flattened by the use of a Quake missile. Those have a high trajectory, so you have to target them at the terraform. They don't pass through shields, even at low charge. Alternatively, the AOE of the Eos or Inferno can be used to do damage through terrain.
Timing and Trajectories
The trajectory of the Shockley and Quake missiles are much higher than those of the Inferno and Eos. Those subsequently have a longer flight time than the latter and can mostly ignore terrain. Make sure to account for the additional flight time of those missiles, firing them at the same time as low trajectory missiles will otherwise result in the latter impacting before the defenses are stunned/the terrain smoothed.
You should never fire multiple missiles simultaneously, as it only has downsides over firing them in quick succession. Repair is compensated by a small extra damage over the stated values. When the enemy has multiple shields, a small delay between missiles ensures that the damage is spread over all shields. Thus the other shields can't block the remaining missiles as they would if the missiles were fired simultaneously.
Fire one Eos, wait 2 seconds, fire other 2 Eos.
Terraformed Shielded Moho
Either fire a Shockley at the shields, wait for it to impact and then finish it off with a Quake followed by an Eos, or try to splash damage it by aiming 2 Eos at either the back of the moho or the base of the terraform.
Fire 2 Shockleys to stun it, finish off with Raiders. Restun with a single Shockley after 40 seconds if needed. The same works for Detriment with 4 Shockleys.