By connecting them to something other than the Matrix. The connection for the audio path between the matrix and the EA5 is just two sets of RCA phono plugs. It's not that the the matrix volumes were "stuck" at zero, you could not change them at from zero no matter what you did (control panels, remotes, iphone app).
Sorry to dredge up an ancient thread, but the problem turned out to be a misapplied software upgrade as near as anybody can tell. This was compounded by an inept and unresponsive dealer. Finally, after giving up trying to get ahold of him and complaining to Control4, they've switched me to another dealer who came out and saw the problem. It took him and an hour or more on the phone with Control4 tech support fix the software on my system and get the thing back up.
I still have the problem that audio3 dies periodically. But this appears to be an unrelated problem.