Starting jDesigner:

It is better to wait for the Thumbnail list blue que meter (above) to complete.
Likely you can do most things in the editor while the meter is still showing. Just that anything Texture related may not work properly.
Keep in mind jDesigner and it predecessors, did not allow
a texture 'thumbnail list' of more than 261 total textures.
In this version it may be limitless!
(Thanks Tom !)

TEXTURE INFO

Right click on ANY texture in the image thumbnail list. 
And the following dialog pops up:

TEXTURE LIST (Tree)

The Master list contain ALL of your textures you have inside the 
GlobalMaterials Directory in you Jet3D install path.
You can't change that portion so we will move on...

1. Creating a new Group

2. Right mouse click in the Texture tree area
and the shown dialog comes up.

3. 'NewGroup' Is the default name.
If you left mouse click once on the NewGroup,
it will be highlighted.

Then you can type in a new name. 
See Group name Suggestions at the bottom of the page

You can I delete a New or Created Group.
Just highlight it 'blue' with the mouse left double click
and press 'delete' on your keyboard. The textures are not deleted, 
just the group name. They stay in the Master list' as you can see.

 4. To add textures to the group, drag the thumbnail image for
below and drop it into the desired 'group' name (windows explorer style)
(Shown below: I dropped two water textures into the newly 
created "Liquids' Group.)

REFRESH TEXTURE LIST

This is for when you add new textures while jDesigner3D is open.
By default when you start Jdesigner, it will 'refresh' the directory tree to 
show ALL Textures that are in the 'Global Materials' Directory on your
 hard drive in your Jet3D install path.

So as to avoid having to restart the application to update the texture list to reflect recent textures you have added in. You can now simply click the "refresh" button:

Then you will be prompter to Save your currently opened jDesigner Map/level.
(shown below)
Choose Yes, if you want the map you are working on saved and reopened. 
No, will open a NEW default cube map.
Cancel will abort the' refresh' function.

Final Thoughts:

Texture doesn't show?
It is in the wrong format. All textures in proper size, 
proportions and color depth will load.
Read the FAQ and 2D artwork section for more info on specifications.

GROUP SUGGESTIONS:
We can categorize our textures to find them faster simply by carefully 
naming your NewGroups.

Here are some suggestion:

Liquids: All water, nuke toxins, lava, etc
Metal: Garage doors, rusty generic metal etc
Earth: Grass, Mud, Cave, Outdoor non-man made.
TERRAIN: Place your landscape textures and heightmaps here.
Sprites: 2D detail object textures. spiderwebs, grates, etc.
Stone: Man made cut or formed rock, concrete, brick, etc.
Skies: You backgrounds, and skybox textures.
Walls-Interior: I use this because of all the indoor specific textures for houses.
Walls-Exterior: Siding, brick, out side building walls.
Roofs: Shingles, Slate, etc. 
Floor: Interior floors, wood, tiles, etc.
Wood: Generic that does not qualify in another category
Doors: Door frames, doors, etc.
Church: I got more specific here since I had many textures only used 
in a church, this is a good idea when you you have specific textures only 
used for one area of a level.
Objects: Textures specific to prefabs or objects for detail. 
Crates, chairs, etc.

- Ken Deel