The map editor is in Zone Mapping mode, single zone editing submode.

A zone simply marks out part of the map; think of it like a map layer with two states per tile: included in the zone, or not. This submode is for editing a single zone at a time. You can place each tile in multiple zones (up to 15) and you can create 9999 zones per map. Zones may be used for restricting NPC movement, and for scripted effects. 

F2 switch to picture mode
F3 switch to passability mode
F4 switch to door placement mode
F5 switch to NPC placement mode
F6 switch to foemap mode
F7 switch to zonemap mode

Z to switch to zone viewing submode.

Use the arrow keys to move around the map.

Use SHIFT+arrow keys to move around the map faster.

Press < and > or PageDown and PageUp to change the current zone number, or type in an ID number. There's no need to use sequential ID numbers.

Press E to go to the zone info editor, where you can edit the triggers attached to this zone.

If the current tool isn't the Draw tool, press + or - to toggle whether you are adding or removing tiles.

At the top right corner the current drawing tool is shown. Press SPACE to draw the zone. The tools are:

D - Draw tool:
  Press SPACE to add or remove the 
  selected tile to the current zone. 
  You can hold down space and move 
  the cursor.

B - Box tool:
  Press SPACE once to place one 
  corner of the box, and SPACE a 
  second time at the opposite corner 
  to add or remove a rectangle of 
  tiles to the zone.

F - Fill (Paint bucket) tool:
  Flood fills the continuous region
  under the cursor of tiles either in
  the zone or not.

P - Paint on Layer # tool:
  Finds the continuous area on the
  current tilemap layer under the
  cursor, and adds/removes all those
  tiles from the zone; like a flood
  fill of a map layer except that the
  map layer isn't modified. You can
  use PageDown and PageUp to change
  the selected layer. For example,
  you could use this to 'paint' a
  road with a zone.

M - Mark tool:
  Use to select a rectangular of the
  map to copy. Press SPACE once to
  place one corner of the rectangle,
  and SPACE a second time at the
  opposite corner. The tool will then
  be changed to the Clone tool. Mark
  copies the visible tilemap layers,
  wallmap, foemap, and zones in the
  rectangle.

C - Clone tool:
  Press SPACE to paste a selection
  copied with the Mark tool.  You can
  switch to different editing modes
  to preview the changes to walls,
  foemap, and zones.  If default
  passability is on (press CTRL+D to
  toggle), the wallmap will updated
  using default walls instead of the
  copied walls.  Only visible map
  layers are modified (press ALT+~ to
  toggle visibility of the current
  map layer), so a map layer has to
  be visible both when Marking and
  when Cloning.

Also,

CTRL+W paints (adds or removes) the tiles visible in the window/screen to/from the zone.

CTRL+Z undoes a change to the tilemap, wallmap, foemap or zonemap. Changes to NPCs and doors are not undoable. The undo history buffer is near-infinite, but certain things cause it to be cleared: resizing the map, deleting or swapping map layers, erasing map data, and leaving the map editor.

CTRL+Y redoes an undone change.

CTRL+S immediately saves, useful when live-previewing a game.

Pressing DELETE removes the selected tile from the zone.

Pressing TAB toggles a minimap that shows the selected zone, and what part of the map you are currently looking at.

~ shows a preview of the entire map.