Is it possible in SSH terminal to copy a folder directory into another directory that will share mostly the same folder names/structure but will have unique files.

In a simple example:

If FOLDER1 has APP > CODE > COM > FILE 1

And FOLDER2 has APP > CODE > COM > FILE 2
THEME > BAH > FILE 3

Is it possible to copy app across 'app' to 'app' so that the files will populate the existing folders and new folders that aren't present will be created in the same structure.

Basically I'm trying to install a module that I would normally do through FTP but I only have SSH access to this new server.

Using scp results in ./app: Directory not empty