I was watching these videos from MIT's series: Green, Stokes.
And I didn't understand the justification: their "extended version" of the theorems.
I looked up on google and couldn't find many references (or they explained things with differential forms, which haven't yet studied).
Does anyone know some references about these versions? I'm not looking for very rigorous/proofy style notes, just some explanation and examples.

For Green's theorem, this page has a good explanation of the technique and a good way to think about the multiple boundaries. And this page goes into more detail about why the technique works. The orientation of the curves is positive if the region is always to the left of the curve in the direction of travel, and you sum the positive line integrals (or negate the terms with negative orientation) to get the integral over the region.
Something similar occurs for Stokes' theorem; I can't find any good references apart from some course notes I don't have permission to reproduce. In general, the positive orientation of the curve is the one where you traverse the curve with your head pointing in the direction of the surface normal and the surface is on your left, and again you sum the positive orientation line integrals (or negate the negative orientation line integrals) to get the integral over the surface.