Do people purposly do this?

I noticed that most of the downloads I get say to extract to Garrysmod/garrysmod and contain two folders: Models and materials. The problem is that when you extract to the folder, the original model and material folders keep you from properly doing this. how do you get past these kind of files?

Actually, it says that the folders will merge, so anything from the addon will be placed in the proper folders, nothing is deleted.