When does the Cowboy Bebop Manga take place within the Anime?
There are actually two mangas for Cowboy Bebop:  


Cowboy Bebop: Shooting Star
This one is supposed to be an alternative telling of the anime series' story. This one has elements of the story as told in the anime and some entirely new elements.
Being 'a new take' on the anime, I guess this one is supposed to replace its timeline.
Source 1 and 2  
Cowboy Bebop
This one features side-stories, which are supposed to be separate from the anime story.
According to Anime News Network, this one is supposed to take place before the ending of the series (but they do not cite any references). It could fit somewhat like the movie does.
Source