Folks, there are 2 ways to deal with a patch in a modded install. Both of them start with a 'clean' install of the program in question.
First technique is in the knowledge base...make a clean install, patch it up, and copy your mods over to it.
The second technique I use. Again take a clean install and patch it up. Now, take a good look at it inside the directories of the clean install. If you notice, most of the files are 'core' files and can't be altered by ANY legal mods...things like exes, dlls, and cat files. If you note, that's most of the directories except for the Objects, Sounds, Controls, Terrain and parts of the main directory.
Copy those unalterable files over from your clean install to your modded install. You can skip the Controls...just go into the WOI menu of your modded install to add your new control options. You can skip Sounds...or copy it over and say "No to all" so you don't overwrite any custom sounds you have but add any new sounds made by the patch.
Basically, if you don't copy over any ini files, you shouldn't break your modded install at all. If you want to copy over the specific ini's affected (objects, terrain,campaigns), you can, but may alter those objects and terrains if you modded those specific objects from stock (ie made the MiG-23 flyable, etc).
It's easy, just a little tedious...and best of all it works and doesn't break anything that wouldn't be broken no matter how you did it (ie if your model would be unflyable in WOI, it's going to be unflyable no matter how you apply the patch).
FastCargo