You can "extract" them with Tile Molester. DS uses the same 4bpp and 8bpp formats as GBA.

The Console Tool (or its current version) can read the metadata in these files and put sprites together with their proper cel and palette data, though there's no insertion/extraction functionality as of yet. But it's useful if you want a preview.

Also, it's not "CEII", it's "Cell". Bit of a typo there.

I think LowLines (who made the Console Tool) has the updated version of that document you posted.
http://llref.emutalk.net/docs/

You might get better ideas if you play around with the Console Tool or CrystalTile2. It depends on the game, so you might try a few different games. If you have individual .NCGR, .NCLR, .NSCR, .NANR, .NCER, etc. in your game file, you can open the .nds rom file in either program. It will list these files with different icons. (Tile icon, pallette icon, etc.)

For Console Tool, you need to click individual files to tell the program what files you want to link together first, then you double-click one of the file to view the picture. For CrystalTile2, you go to Tools/File System first, then select View/Tile Viewer and then right-click a file on File System window to view the picture or the map, etc.

(Not a very good explanation here, but you can try the programs and you'll probably understand what I mean. ^_^)

Note: Not all NDS games come with simple graphic formats that you can open with these programs. You might try to find a game with simple format first if you want to study the structure.

Basically, you will either see

NCGR = your tiles (picture)
NCLR = your pallette
NSCR = your map

or

NCGR = your tiles (picture)
NCLR = your pallette
NANR + NCER = your animation (think of them as sprite controller.)

You can import/export the pictures with CrystalTile2.