How would you convert .mts files into smaller h264-files - keeping the same file structure?

We are working on a movie project.
For the project we have created a quite handy file structure.

Example:

\trip 1\New York\Story 1\ Camera 1\0001.mts
\trip 1\New York\Story 1\ Camera 2\0001.mts
\trip 1\New York\Story 1\ Camera 3\0001.mts

Of course we have a camera 2, Camera 3 and so forth folder.

Now I wanted to convert our files into a smaller working version to work with it in premiere CS6. But in order to make relinking easier, I wish I could convert the files by dragging the folders into Adobe Encoder as a whole and it would duplicate the folder structure such as examplified above.

Example for converted folders:

\trip 1 CONVERTED\New York\Story 1\ Camera 1\0001.mov
\trip 1 CONVERTED\New York\Story 1\ Camera 2\0001.mov
\trip 1 CONVERTED\New York\Story 1\ Camera 3\0001.mov

I know this sounds all very complicated – but I just really want to convert my mts files to another destination, keeping the file structure.

Impossible to google and the manuals of Adobe seriously suck.

Help so much appreciated!