The structure of the show is pretty weird. You can kind of interpret the series and the movie being two different views of the same ending. The series essentially ends by showing you how things play out really specific to Shinji's perspective, largely focusing on his mental state and what is happening in his head.
The movie tells a lot of the same events, but steps back and tells it from a much more broad perspective. This shows what is physically happening throughout the time that Shinji is having his mental breakdown and figuring things out at the end of the series. As such, some plot points relating to Shinji are shown happening again but with a much different context.
But does it all make sense? I mean, kind of but also kind of not. I think you're supposed to feel what happens more than you are supposed to understand it, but all of the things that you are asking "where did this happen" I do think are explained to some extent, or at least heavily implied. It is hard to parse the relevant information from a lot of the crazy shit thats going down, so it definitely takes multiple watches to fully grasp, and even then, it is largely supposed to be interpretive and not exactly literal, so if you are the type of person who needs your story to be straightforward and literal, you aren't going to get that from Eva.
Thats also part of what makes it so amazing in my opinion. I don't think there is anything else like Eva in anime. It is a singular trip with an insane artistic vision and I respect the hell out of it for that.










