I'll be more specific;
The replacement textures 00, 01, 02, 03, 04, 05, 06, 08, and 12(.dds) should go in ..\textures\terrain\ground
The replacement textures foam, foam00, and foam01 should go in ..\textures\terrain
So for you, delete the "Waves" folder it is only a reference folder, leave the foam files where they are and move files 00, 01, etc... into the ground folder and you'll be done. If you learn the folders/folder structure you will see you are purely overwriting files.
Good luck

K.