Get the program here -
http://www.chaosincarnate.net/cannonfodder/cftools.htm or on our downloads page
Open WinBSPzip.exe, here is the new window.
Now goto file and OpenBSP. Choose the map you wish to include your custom content in.
Now you will see a list of files already included in your map, such as Valve textures and cudemaps.
Now we need to add custom content. In this example I will be loading a soundscape file, since this step is needed to make sure your custom soundscape manifest are not over written by someone installing a new map.
Since only have 2 files in one directory and I will be using both of those I am choosing to Add Directory from the Add Files menu.
Click the ... button to open navigation mode to find your directory.
Now WinBSPzip knows what folder you are looking in. Click Select. IF YOU DO NOT have sub folders under scripts then do not add anything in the line below. Scripts IS the first folder under the MODs folder. Click ok once you are sure you have placed the correct information. If you mess up then you will have to start all over again. You cannot delete mistakes.
You can see I was playing around and got a 2nd copy of the soundscapes in there. The only way to fix this is to close WinBSPzip without saving and start over. You can see here that WinBSPzip knows that you are in the MOD's folder and is using relative pathing. It knows you are looking at the files inside the scripts folder.
How to add a sub folder for materials example.
I, myself, choose to include all my custom textures in one folder, so that I only have to be concerned with one folder, instead of hunting and pecking for single files in multiple folders.
As you can read in the note when adding a directory it must start in the MOD's folder. So the first folder in the MOD's directory is materials, WinBSPzip already knows you are looking in the sub folder.
If your happy with the list then File and SaveBSP. I would recommend you play with a sample file first instead of your real map. IF you screw up then will need a new BSP file as you cannot unwrite once written and saved too.