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

You can place each tile in multiple zones (up to 15) and you can create 9999 zones per map; in this submode you sets the tiles in a single zone at a time.

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

M switch to zone editor submode.

Use the arrow keys to move around the map.

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

Press < and > 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:

CTRL+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.

CTRL+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.

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

CTRL+P - Paint on Tilemap tool:
  Finds the continuous area on the 
  current tilemap layer (you can't 
  select or see which layer is 
  selected without switching to 
  Tilemap Editing mode) under the 
  cursor, and adds/removes all those
  tiles to the zone.

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.