Hello Jesus,
I do not know of courses or tutorials about optimization on manifolds that exist in video, unfortunately. That would be nice to create at some point.
For the specific concepts you brought up (atlases, submanifolds and quotient manifold), I expect that there should exist good introductory courses for differential geometry on either coursera, or edX, or MIT OCW, or others, that would cover this in accessible terms. I do not know of any in particular to recommend, but if you find one you liked, it would be great if you could tell us about it here.
About atlases in particular, I would also add that they are never used in practice, only in theory. Of course, they are a necessary tool to understand even just the definition of manifolds, but using the somewhat higher level notion that "a manifold can be linearized at every point, into a tangent space", you can get a long way in gaining high level understanding.
Best,
Nicolas