Hi Commando, welcome to the "fast-paced" world of island editing!
The will be loads on this in the manual, but just in case you didnt understand it...
The 1.46 islands already come with their own seperate configs, in a .pbo in DTA folder, so what I did was unPbo'ed every file in the DTA folder, and put them in the WRPTool object/texture directory, where it asks you to put it.
Hope I helped a little,
AnarCHy