First, unpack the archives if you haven't already, and don't forget the us sysstrings. on the top, you can select the original rootR (or possibly other files) and the folder where you have unpacked your files.
you can use two different folders for jp and us files (so you don't have to move any files) or you can use a mixed one just as before. If you have unpacked to separate folders, you have to select the the folder at the top where the two folders are, select the second option in the middle (use different folders) and set the name of the folders. For example, if you have unpacked to C:/rootRs/jp and C:/rootRs/us you have to select C:/rootRs at the top, and write jp and us as folder names.
Check the undub options if you want then press the "Export listfile" button. You can use that listfile right away for repacking. Then press the Repack button and you can save the cpk. The message log will update when it's done (because i haven't managed to do it correctly with threading).
Note: Exported listfiles are only for JP rootR, but you can use your own files too.
Edit: I left out two letters from the bat file, here is the fix.