Most ideas for maps start off as a fresh empty map. And build your geometry from there.
To get you started on textures, copy the Sample map into your missions folder, rename the folder to you map for example "Island_Estate". And rename the Wad file found in the mission/textures folder to your map name.
When you add textures to the Wad file, you are essentially adding textures to your map, once you use the texture, the texture must exist in the textures folder before building your map in WC. All Textures need to be 24bit and a power of 2.
Wad files are edited using Wally. If you are using the wad file in WC, it can only be edited if WC is closed.
The dat files are necessary to add functionality. The dat files also are necesary for swat3 to run the map. One file in particular is the missioninfo.dat.
For information about this, and more. Visit the FAQ pages in you Swat 3 installation, or Visit us on TeamSpeak, we will do our best to explain it.
If you have a few minutes I will be on TeamSpeak. I have not tested WorldCraft nor the mapping tools on the GOG version, since I own and use the original TGOTY edition. It might work but the directories might be a little different.