There is no automatic solution to your problem. You have to create two comps. One at the standard frame ratio and frame size for mobile devices, and one at a standard frame ratio and frame size for desktop video. You CANNOT precisely match every mobile device or display screen, but you can follow the general guidelines. Then you need to render to an industry-standard compression format. Unless you are an expert in video formats, standards, and compression technology, don't create custom sizes, use the published standards. Check YouTube or Vimeo for the standards for vertical format video. I don't have time to look them up.
In some cases, you can just nest your standard horizontal format comp inside the vertical comp and make some adjustments to scale and framing. In other projects, you are stuck with doing two completely different animations.
At IBC this year a demo was made of an upcoming feature in Premiere Pro that automatically creates multiple sequences from a master edit for different screen sizes. This is an upcoming feature so look for it in the next release or two.
I would also suggest that you do most of your editing in Premiere Pro. AE is incredibly hard to manage if you try and edit a movie or an explainer video in the comp panel. AE is designed for and only good at creating shots, motion graphics, and in some cases short sequences that cannot be created in any other way. Almost all of my comps are under seven seconds long and one shot. On rare occasions, I'll create a comp that contains a full sentence or phrase of audio, but I would almost never do a single AE comp that was over a minute long. If I were doing your video, from looking at the samples, I would create a separate comp for each of the new screens that pop up, render the results, then put the project together in Premiere Pro. You'll have a lot more control over the edit, the timing, and the final project will not only be easier to manage, but it will take a lot less time to produce.
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