"It seemed like the worst-kept secret that things were weird between them," a set source tells PEOPLE in this week's cover story.
In the wake of their separation announcement this week – and Arquette's recent revelations about the couple's issues and their sex life to Howard Stern – friends of the famously mismatched pair say they always had differences but seemed to work through them.
Now, however, both Arquette, 39, and Cox, 46, are figuring out where to go from here.
"This was not an overnight thing," a source close to the pair says of their trial separation. "They needed to figure things out and try to find a happy place again."
For much more on this story, pick up this week's issue of PEOPLE, on newsstands Friday