During the actual fight the Zerker will charge at you or your teammates. Whilst it is running it's chest/ribs will open up, and your aiming reticule will turn red. This is the time to shoot it.
This can be a very long battle, especially on the higher difficulties but there is plenty of ammo around the 'arena' as well an unlimited ammo stash at the back left corner (As you enter from the door).
Once you've dealt enough damage the Zerker will leak imulsion, this does pretty hefty damage on you and on Insane dfficulty it will instantly kill you. So you'll be wanting to avoid the Zerker until the imusltion trails disappear. You are in a circle shaped area and you can easily get away from the Zerker by going around the other side.
Towards the end of the battle the Zerker will leak imulsion vapor, this is exactly the same as the trails but will damage you more. So once again, avoid it.