Adding Folders to File Name, then Make Folders from Filename

I have a large number of files in various folders and subfolders that I need to batch process through a tool that doesn't retain paths. /this/that/and/this.ext winds up as /this.ext. I want to preserve the folder structure, so I thought I'd use Hazel to...
1. Rename the files to include the path in their filenames.
2. Move the renamed files to an inbox for the batch tool.
3. Execute the batch tool (manually or by triggering with Hazel when files are in the inbox)
4. Take the output from the tool and parse their file names back into paths.

The problem? I have no idea how to do any of this. Please help?

Here's the path to a single example file.
/Volumes/Media Drive/Comic Books/__IN To Be Compressed/Marvel Noir/Iron Man Noir/Iron Man Noir 04 (of 04) (2010).cbr

I want to be able to send that through the batch compression tool and then get it back to that full path again. It seems to me the best way to do that is with the above process, but I don't know how to build the rules in Hazel to make that work.

I'm a bit unclear on the exact details here. Also, what batch compression tool are you using? Can you give an example of how the example file you gave would not work with the path it has?