OK from what i can tell we've seen in total 4 of the 6 hatches on the island (i say 6 as the orientation video for the swan is 3 of 6 i think)
The Swan The Arrow The Pearl The medical station where Kate, Rousseau and Claire go in the episode maternal love
Now my questions are 1) what was the Arrow used for and 2) what is the name of the medical station, it's abanndoned now but it has a kind of red sword as a logo, there's probably and image on google.
I've also now discovered, by pausing theDVD on the episode Lockdown, that there is a hatch or bunker thing caled the flame, or something similar. Two of the other parts of the map on this episode are hidden from view which is a bit of a bind but no doubt S3 will bring us answers.