I'm wondering if I'm even approaching this properly.
Depends on how complex the 3D model is and of course how much time and resources you actually have to deal with the 3D part. AE can of course sort of import models using Cinema 4D Lite/ Cineware, but even that is limited. Conversely, 3D plug-ins like Element 3D are limited by their capabilities in how many polygons they can render via your graphics card. And then of course all that other stuff with setting up materials, textures, lighting. Either way, usually people start out in their 3D programs, including modeling teh geometry, tracking the camera and setting up everything. Then you simply render images from there which you overlay onto the footage in your compositing tool and if need be, of course you then could export your existing 3D scene as well for additional work. Still, it may be perfectly possible to e.g. visualize a basic family home using just AE and soem 3D plug-in magic...
The very first thing you need to do when approaching this kind of job is to remove the lens distortion from your aerial footage. If lens profiles do not exist then you will have to photograph some charts and figure out exactly how to remove all of the distortion from the shot.
Once you have the distortion removed an accurate camera track can be extracted. Once you have the accurate camera track it's just a matter of integrating the tracking information and the 3-D program.
Approaching this problem without fixing lens distortion is going to cause you all kinds of problems.
Depending on the shot You may also be better off using a program like Syntheyrs to do your tracking.
There are also programs out there that will allow you to generate very accurate 3-D models from drone footage. I have used these services for expert witnessing work a couple of times. Drone Deploy Is one service you can use. I will be using them in the next couple of weeks for a job. DroneDeploy: Powerful Drone & UAV Mapping Software
Element 3d, as Mylenium mentions, is quite a popular plugin for adding 3d objects to After Effects. They even have a few tutorials for putting their models into motion tracked footage.
However, if you'd prefer to work without paid third-party plugins, Cinema 4D Lite (which he also mentions) comes free with AE and can do this too. See this (free!) tutorial series for getting up to speed on using it.
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