Editorial manager (And Manuscript Central) now forces LaTeX submissions to be submitted as raw LaTeX files, which sounds easier than it is.
After spending many hours figuring this out, I thought I'd share my learnings.
1. Move all your figures and style files out of the subfolders to the root folder (and obviously change the tex to point to the new location).
2. When uploading select the tex files, bib files and style files as "Manuscript".
3. Select the figures as "Figure"
4. Do no upload your compiled PDF, the system generates that for you.
Here is a video to demonstrate how to do it: https://youtu.be/85cm-BXt5EE