To be honest it's kind of hard to explain. It's definitely after season two, but you definitely have to read the manga because the movie is after the Manga Arc that is currently in the manga. In the movie they talk about Natsucomi, but the manga isn't even at that part yet.
Long story short, the movie is WAY ahead of the manga, I think.
hmm.... so its just okay to wait for season 3 and watch it?
[Well cant be sure yet from which chapter season 3 will be xD if there will be skip il make topic on season 3 when its out and ask if anything got skipped]
That's very weird, so it's basically some kind of separate movie? I hope though that they won't suddenly put in characters that haven't appeared in the other 2 anime, but I think it's acceptable if they did since I should just read the manga.
Season 2 ended with the end of the school year, which I think is late March/April for Japan. The manga continues the story up through something like early August, I think. This movie seems to be late August, so the manga itself hasn't caught up to the movie.
So far, the both anime seasons combined have only gone through almost 150 chapters of the manga (although some of the chapters were skipped over). The order the chapters were done is a little messed up, especially because the first season decided to make a whole year go by, which was fixed by Season 2. For example, things like the New Year's drive to the beach, Nagi selling Hayate to Isumi, etc. actually happened BEFORE Hayate ever met Hinagiku and the others at Hakuo (it was winter break, after all). Some of the filler episodes of season 1 actually take place in between events of Season 2, like when they go fishing and Maria catches that huge carp.
Overall though, the 70 or so episodes combined make up only 150 out of the currently 350 chapters in the manga, so a Season 3 will likely only cover a portion of the manga. Furthermore, the manga will continue to get longer by the time they actually make a Season 3, and eventually the manga will catch up to the events of this movie.