You can't change the filenames or alter the default naming system. The iPhone mode is shown in the Info window, but if you have the same model that won't help. It looks like you can't even search by iPhone model. There's also no method of assigning captions in batches.
If you have a Mac you can use scripts to batch change captions and titles.
How are you combining the pictures? Are you using the same Apple account? Or are the pictures combined later?
One thing I think of is to make one set of pictures 4x3, and the other 16x9, or something like that. "Revert" will bring them back to the natural size of the sensor, but in the mean time they would be marked by their size. Or you could mark one set as favorites and not the other. A bit lame…
If you have suggestions for Apple, you can leave them here:
Feedback - Photos - Apple