Merging...

AFAIR you can do this, but it's buggy. Can't remember the method (google it!).

Best thing is to manually move from smaller folders into the main one, it also gives one a chance to manually check for conflicts (e.g. files with same name and the version of the same file is the one you actually want), BEFORE dumping a whole folder's contents into another. Otherwise you simply get a nondescript pop-up saying something like "File x is already in this folder, do you want to replace: Yes / Stop" before it moves on to the next conflict.

 

In El Capitan:

Merge two folders with the same name
If you have two folders with identical names at two different locations, you can merge them into a single folder.

Hold down the Option key, then drag one folder to the location that contains a folder with the same name. In the dialog that appears, click Merge.

The Merge option appears only if one of the folders contains items that are not in the other folder. If the folders contain different versions of identically named files, the only options are Stop or Replace.

To organize your files automatically, use Smart Folders. Smart Folders automatically gather files by type and subject matter, and are instantly updated as you change, add, and remove files on your Mac.