There is no set time schedule in particular to the Animatrix series.
Some episodes, like the Final Flight of the Osiris, happen between M1 and M2, and directly kick off the first events in Enter The Matrix. Its one of the first missions you play, trying to get to the Post Office to pick up the transmission from Thadeus.Stuff like The Second Rennaisance( Pt.I & II) are part of the Zion Archive, when man still ruled the Earth and we invented A.I., then the conflict and proceeding war.Think about 'Dead Man Clapping'- still gives me chills....
Detective story was about Trinity the hacker, whilst in the Matrix, way after the machines had produced the fetuses. Kinda like Neo, in M1.
The rest are either almost like Construct programs, or centre around people being aware of the Matrix and trying to escape (Kids Story for example)
There is no set timeline in Animatrix, its all configured randomly(very Nostradamus).
However, with all else, it sits, M1, M-Rel & ETM simultaneously, leading at the exact moment to the beginning of M-Rev.....
i thought about getting a few vhs tapes, starting with the second renaissance, and putting all the matrix stuff in order like that... fusing together the 3 movies, but having the osiris scenes between m1 and reloaded (as well as kids story)... i think that would be an awesome set of tapes, also displaying the use of so many mediums to tell the story.