Secret door system works in two different ways. The first way is used in the building of the module, and the another is used when secret doors are created on the fly by the dm.
The module version includes Secret Trigger trigger on the area. When player enters that area a skill check is done and if it is successfull then secret door is revealed. The secret door is controlled by the variables set on this trigger. There is two mandatory variables, secret_dc and secret_resref. The secret_dc gives the DC of the detection of the door, and the secret_resref specifies what kind of secret door is created. There are several different door types. Doors placed on the walls are ztk_secret_w_w (wooden), ztk_secret_w_m (metal) and ztk_secret_w_s (stone). Trapdoors placed on the floor are ztk_secret_t_w (wooden), ztk_secret_t_s (stone), ztk_secret_t_g (grate), and ztk_secret_t_gs (stone grate). There is also ztk_secret_t_001 (secret path) and ztk_secret_track (hidden path tracks).
In addition to those variables, you also need to give either locations or waypoint name of the location where the waypoint is created and destination where it transfers you to. In the module version you normally use waypoint names, in the dm tool version you normally use stored location.
There are several other variables which can be used on the door and they are documented in the variables on the Secret doors section.
When used with the dm tools instead of using a trigger (those cannot be generated dynamically by scripts) it uses a hidden creature that will do the reveal checks when it perceives players.
There is tools DM Secret Helper (currently dmsecret_helper under Special 5 section, should be moved to the Tutorial section and renamed to DM Secret Helper).
To create secret doors, you need to first store 2 locations, the first one which is used as a location of the created door, and the other is used as destination where the door transfers you. This can be done by first targetting the ground where you want the secret door to transfer, and then select from the menu option 1 Copy current target to stored location 1. Then you can jump to the place where you want the secret door to appear and use the tool again on the ground, and select menu option 2 Copy current target to stored location 2. Note, that if you want to create wall doors, make sure you are facing exaclty to the wall where you want it to appear.
When you have those 2 locations stored, you can then create the actual secret detector creature. To do that use the tool again on the ground close to the place where you put the second location (i.e. normally people need to come close to the door before they can detect it), and select option 4 Create secret detection creature here.
After that the tool immediately goes to the menu that allows you to modify the properties of the secret door. Normally you want to set the DC to be something suitable for the group. The skill can be the default Search unless there is real reason to select some other skill (for example hidden magical portal could use spellcraft instead. Class and level based secret doors are not normally used in the dm quests (i.e. those doors are found by specific class of more than given level (+1d4)).
The next thing you need to do is to set the locations, i.e select option 6 Set locations, and copy one of the stored locations to the location of the door, and another stored location to the destination.
After that you can set the door type, and in the Other things you can set the animation type to match the door type (low for trap doors, and middle for the wall doors). Also you might want to set the announcement on, which means that when someone detects the door he uses voice chat to announce it. If you want the door to disappear after some time, set the reset time to match the time how long you want the door to stay visibile.
If you want to modify the existing door simply target the created secret detector creature, or the revealed door.
So in short to create secret door do following:
This tool do need some more work to make it easier to use and allow it to modify other things on the doors too. Actually we need one generic Door helper, that can be used to set settings of the any doors normal or secret doors.