The map editor is in Picture mode (also known as "Tilemap mode").

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
F8 show settings menu

Use the arrow keys or RIGHT CLICK and drag to move around the map.

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

Use ALT+arrow keys to move the view of the map.

Along the top of the screen you will see a row of maptiles, with your currently selected maptile highlighted. You can click on them, press < and > to change your selected maptile, or use the MOUSE WHEEL, or press ENTER or RIGHT CLICK on the top bar to bring up a full-screen maptile picker.

Press G or RIGHT CLICK if you want to get the tile under the cursor as the current tile to place.

At the top right corner the current drawing tool is shown. Press SPACE or LEFT CLICK to draw on the current map layer. The tools are:

D - Draw tool:
  Place a maptile on the map. Hold 
  down SPACE and move, or drag the
  mouse to draw lines.

B - Box tool:
  Press SPACE/CLICK once to place one 
  corner of the box, and SPACE/CLICK 
  a second time at the opposite
  corner to draw a rectangle of
  tiles.

F - Fill (Paint bucket) tool:
  Flood fills a continuous region (on
  current layer) under the cursor 
  with the current tile.

R - Replace tool:
  Replaces completely across the 
  whole map layer all tiles like the 
  one under the cursor with the 
  current tile.

M - Mark tool:
  Use to select a rectangular of the
  map to copy. Press SPACE/CLICK once
  to place one corner of the
  rectangle, and SPACE/CLICK 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/CLICK 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.

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.

~ shows a preview of the entire map.

TAB toggles a blue rectangle that shows roughly what portion of the map you are currently looking at.

CTRL+G toggles whether a tile grid is visible (change the color in the Editor Settings menu).

CTRL+O shows an outline indicating where the edges of screen will be in-game, when the hero is standing on the current tile. Use this to check what wil be visible. Press CTRL+O to make the outline follow the cursor. (This option is also in the F8 menu.)

CTRL+N toggles whethers NPCs are visible.

CTRL+H moves the hero's starting location to this location on this map. Remember that only one map in your game needs a hero starting location.

Press 1 or 2 to make the tile under the cursor animate using animation pattern 0 or 1.

Hold CTRL and press 1 or 2 to make all tiles on the current layer like the one under the cursor animate using animation pattern 0 or 1.

CTRL+D toggles whether default tile passability (which you assign to tiles in the tileset editor) will be used for any new tiles that you place.

--------------------
---- Map layers ----

CTRL+L opens the Layer menu, where you can change tilesets and layer visibility and add or name layers.

PageUp and PageDown change which layer you are working on. Remember that layer 0 is the bottommost. (You can also use CTRL+period and CTRL+comma in case you are one of those poor souls with a laptop that doesn't have PageUp and PageDown keys!)

Or hold CTRL or hold the LEFT or RIGHT MOUSE button and use the MOUSE WHEEL to change map layer.

CTRL+J makes the current layer jiggle. This can be useful to visually distinguish a layer you are working on from another layer that covers it up. Press CTRL+J again to stop the jiggling.

ALT+~ toggles visibility of the current map layer.

ALT+# (a number key) disables or enables that layer (you can't disable layer 0). Disabled layers aren't drawn while editing or playing.

CTRL+F# toggles visibility of a layer: F1 is layer 0, and so on.

Hold CTRL+SHIFT and press arrow keys, or press CTRL and drag with the RIGHT MOUSE button, to "skew" the map layers, drawing them with a 3D perspective so that you can tell them apart.

T tints the map layers, so that you can tell them apart. 
Press T once to tint by layer height: from layer 0 to the topmost (including overhead tiles), tints shift through cyan, green, yellow, red and purple.
Press T twice to make layers other than the selected one grey.
Press T again to cancel.

-------------------

CTRL+BACKSPACE deletes everything placed at a tile: tiles in all layers, walls, doors, and NPCs. But not zones.

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

CTRL+W paints the tiles visible in the window/screen with the current tile.

Any tiles that have the obsolete overhead bit set will be marked with O's if you are using multiple layers. This is normally a mistake: Use layers instead of `overhead' tiles!