Hmmmm.... I mean, how to make a texture pack :3
And what software to edit a texture pack :3
Hahahaha sorry for bad english XD
To make a texture pack you have to edit all the textures in pokemon 3d.
They are in .xnb format if you didnt notice already.
http://pokemon3d.net/threads/408/
Is where you can get the tools.
To make a texture pack you will need xnb exporter and xna formatter
Put the .xnb exporter in the folder where you want to "export" the textures.
This program is just a one file thing, so copy and paste it all you please.
For this example, we'll put it in the following directory
Pokemon/Content/Textures
Now, export the "routes" texture.
You will need a program like gimp, photoshop, etc. to make some of the textures transparent.
Once you edit the textures to your liking, go ahead and add the transparency, and you're done.
Then, open the xna formatter and use it to make the .png file you editted an .xnb file.
This will not delete your .png file, but it will overwrite your default p3d .xnb file.
So, i highly recommend downloading a second p3d for textures, or just making a backup folder (I have about 6 different pokemon3d files on my computer)
Open the game and test them. Rinse and repeat.
If you have questions, just ask.