It is a while since I have even looked at the old CFS1 tools
They use the filenames to perform matching. The only way I can think is to use the same filenames for your custom textures as for the default. This is complicated though as the filenames tell you not only what class of terrain this is but also which other classes each edge "matches" with. Unless you design your custom textures in exactly the same ways as the default then the auto tools are never going to work successfully.
