When does a mod override vanilla assets?

You can overwrite files by using the same file names in the root of the vehicle folder. That's the easiest case to fix.
Another way to overwrite things is using the same material names/mapping/persistentIDs in your custom material file or using the same jbeam block names. For example in your custom etk800_engineMOD.jbeam you will keep the original oil pan block with the same name. It will overwrite jbeam from the original file even if the file itself is different.

You can put your files in subfolders, then you don't need to worry about filenames, but jbeam block names/materials issue still applies here and you need to remember to remove not changed parts of jbeam like my oil pan example or if you edit it you need to change its name by adding some suffix for example.

As for file structure, you need to put your files in the respective vehicle directory, for example, \vehicles\etk800\ or \vehicles\etk800\my_mod\, otherwise it won't load correctly.

 

A mod overrides vanilla content when at least one of the following criteria is met:

• It has a folder with the same name as one of the vehicle folder, and one of the files has the same name and sub-path location as a file in the original vehicle folder, then it will override it
• It has a folder with the same name as one of the vehicle folder, which contains a Jbeam file that has a part with the same name as one that exists in the vehicle, it overrides the part then
  
• It has a material with the same name or mapTo as a material that exists in a vehicle in game, it overrides that material then
• It has a .dae, .cdae or cached.dts file containing a model of a vehicle part with the same name as one that exists on any vehicle, then the one that is spawned first will override all other ones

 

Usually you can change 1 character in the persistentId and there will be a very high chance it won't override anything. And the full results of the checker are in the log file in your userfolder.

 

The best approach is completely removing persistentID line from material and then resaving it with the game, it will generate and save a new proper PID.