Hi,
It's very difficult to answer your questions in this format as it would take pages and pages of instructions and explanations &
it's likely even the explanations will require explanations.
Learning After Effects, like many other CG softwares, is a cumulative process, like math.
You can't start with trigonometry; you have to first study and understand basic arithmetic, algebra & geometry.
Fortunately, Element 3D is one plug-in for which there are lots of high quality tutorials from Video Copilot and Andrew Kramer
both on VC's Youtube channel and on their website as well. Unfortunately, VC's tutorials are generally much longer than Lynda's, which generally last about 6 minutes. VC's tutorials usually run about 30 minutes to an hour and have the prerequisite of possessing an intermediate understanding of After Effects. Also, they will not necessarily teach exactly what you want to know. Rather they will give examples that cover how to use the software. What you see in that video requires understanding of basic (not simple) principles of animation, lighting, cameras. Following Video Copilots tutorials on using Element 3D fully cover how to create and animate 3D objects using their softwares UI so you can use them to create what you want.
In addition to learning which buttons to hit in the plug-in's controls (User Interface (UI)), you may need to create lights and 3d cameras & various production "post effects". All of this requires much, much more than just knowing which buttons to press. Creating a light is easy, but knowing how to effectively light a scene is much more difficult. Setting key frames is easy, but understanding basic animation principles so your animations will look great can take years of study & practice.
OK...so if you've made it this far and are not yet discouraged, here's a few tips:
1) The letter flying in past the camera & into place.- Animations like this are much easier to do in reverse. You create the 3D text in it's final position and set key frame for all the properties (in all 3 dimension) at the place in the timeline where you want them to be fully in place. Then you move the current time indicator (CTI) back in time and move each letter out & past (behind ) the 3d camera, adding rotation. Now when you play the animation forward the letters will fly in from behind the camera, rotating & land in place.
2) The timing & placement of the words and rocks - Study the 12 principles of animation: 12 basic principles of animation - Wikipedia
and practice...alot
3) The lights can be several effects...3d light rays, multiple layers of various types of animated noise with glows blended, optical flares, light leaks, etc.
So, if you've made it this far and are still not yet discouraged here's the last thing: That template is high end work. There's ALOT going on and each element could have been achieved multiple ways with multiple tools. The letters were likely done with Element 3D (since they're the part of the template that are dynamic (editable)) but other elements could have been done with other tools.
For a beginner to ask how to make something like what they see in this template is simply unreasonable.
It's like someone asking how to build a spaceship because they saw Star Wars.
To be able to make something like what's in this video requires literally years of study and practice.
I would suggest a different approach to learning. Looking for a lesson that tells him what he needs to know to create what he wants is a bad approach because he doesn't yet know enough to know what he needs to know.
Instead find a reputable learning path...whether it be Lynda.com, Pluralshight or a full 4 year university and follow the curriculum dictated by the instructors, not by the student.
Just like with math: Arithmetic. Then Algebra. Then Geometry. Then Trig. If you try to skip the prerequisites you will not be able understand. There are exceptions, of course, for the exceptional.
But if your son is hell bent on trying, I suggest purchasing the template and reverse engineering it. Just look at it sand see how it was done. If he can;t, then I suggest he go back and spend a few years doing what's in the tutorials that ARE available. Understanding that the "broadness" is to his ultimate advantage & that once he possesses those "broad skills" he can then choose to focus them on whatever he wants.