It's quite easy if you see the other configurable options already on the registry.
I will explain the procedure I've succesfully used on win98se.
WARNING:
Screwing up the registry is crappity smacking up your windows installation, so be carefull. Although if you only change the stuff I say nothing bad could happen, I ACCEPT NO RESPONSABILITY FOR DAMAGES OR ANYTHING!1.- Open the windows registry editor (regedit.exe in the windows folder)
2.- Browse the registry to "HKEY_LOCAL_MACHINE\System\CurrentControlSet\Services\Class\Display"
3.- Inside this place, locate your voodoo card device number which holds folders and settings for your card, it could be either 0000, 0001, 0002 etc.. depending on what display adapters you have installed on your system before the voodoo.
4.- Go inside the registry "folder" that you want to add an advanced feature for, this could be "D3D" for direct3D settings or "Glide" for OpenGL/Glide stuff. I haven't tested adding stuff on the "DEFAULT" registry folder, but I guess that anything added there will appear on the "General" section.
5.- CLOSE 3DFXTOOLS RUNNING PROGRAMS IF ANY
6.- From there add a registry key named as you want (suppossed to be descriptive), for example "3dfx Watermark" on \Glide registry key.
7.- Add registry values as needed, you can simply mimetize the settings for any other tweak already there, for our example we just need a Enable/Disable simple thing. You can see my registry for this example on the following screenshot:

Don't forget any entry or it may not work. The most relevant value is the "Tweak Value" entry, which MUST correspond to the registry tweak you want to be applied on that registry folder (Glide/D3D), you can search the web (falconfly archive has a list of possible values) for possible tweaks. All registry values there MUST BE of string type even if they are numbers, don't use binary or DWORD (double word) stuff at all or it won't work.
Thats it, now run 3dxtools hub and you will see the "3dfx Watermark" option on your 3dfx advanced features list, under OpenGL/Glide.
(Corrections/comments are welcome)