Alright, so I opened up my Gtk, and I think I know what you should do. Open it up, select Jedi Academy for the game you are mapping for. Once it's open, click on "File" at the very top. Scroll down to "Project Settings", and click it. Under Project Settings, you will see it says, "Basepath", followed by a bar. Click on that bar, and input the location of your jedi academy/gamedata/base folder, then press "OK" on the top right hand side. That should do it.
EDIT:
So you know what to do from here, keep reading.
Once you establish where the destination path for the base folder is, make a box or whatever. At the top, click on "Textures", it is on the same place as you found "File" from before. Once you click on Textures, scroll down and select the texture folder you wish to use. Now select the box (when making a new box it should automatically be selected), and press "T". T is the hotkey to bring up the texture application window. Double click the texture you want, and ta-da. You have a textured box.
There once was a member of this land,
A humerous posting he had planned.
But when he posted,
By mods he was toasted,
And he had found himself banned.