The marketing of this game has a lot to do with the popularity of the first game and the hidden meaning that is looked for throughout both Portal and Portal 2. The big question is where the co-op story takes place during the main story. There are three possible places the co-op story line could have taken place. The first and most unlikely is the co-op story takes place before the original Portal game. This is possible because at the end of Portal 2 co-op the player sees all the humans stored within tanks. Could Chell be among them?
The second possible placement for the co-op storyline would be shortly after GLaDOS awakens in the Portal 2 storyline. This is more noticable after someone has played through the single player compaign and then the co-op. Some GLaDOS says in the co-op come up in the single player, like when she discusses seeing a deer on the surface.
The final placement possible is after Portal 2 and it seems to be the most likely, however it is not definate. GLaDOS is in full control of Aperture, she makes vague references to Chell, therefor GLaDOS would need more test subjects since this would put Chell no longer within Aperture.