How should we be keeping track of secret doors?
Assuming you are playing the new WotC version, the rules state


  You might wish to keep track of the doors you found on a piece of
  scrap paper


Now all you need is some way to easily reference a specific door.  You could try to describe the area it is in, like "Door to east-most level 4 room". 

Of course, if you're playing the older "New Dungeon", it wouldn't really be a problem, because in that version you forgot about secret doors as soon as you moved away from them.