There are multiple ways, depending on what you want. I'll split the post into multiple goals even though you already stated what your goal is. This is more for other people finding this post and maybe you change strategy and decide to use one of the other options instead.
Merge folders into a new location
I'll start with what you want to achieve. Basically, you can just copy the folders from drive 1 to drive 3, then repeat the process for drive 2 and copy those to drive 3. The second time, Windows will say: hey, this folder already exists. Do you want to overwrite? When saying yes, it will overwrite the folders and merge the old and new content together. If a file with the same name exists in both folders, it will again ask you if you want to overwrite, skip or rename. Depending on what the data is, choose the best option for you.
Show the content of 2 locations as if they are 1 location
From windows 7 and onwards, you can add a library. A library is a collection of folders that is shown as one huge folder, divided by the folders. The beauty of this principle is, that you can switch to group by location, or sort on filename, or more, depending on what you need at that moment.
Simply right-click the folder you want to have in a library, choose include in library, then choose create new library. Give it a name, then repeat the same with another folder that you want to include in that library, but instead of choosing create new library, select the freshly created library instead.
