|I've found a way. Although its a very very long way to do what I want.|
1. use a auto renamer to make all files have almost the same file name like "nameep1.mkv" "nameep2.mkv"
2. Do what You want done with the first file in Mkvmerge (Including the output directory) but dont click the start muxing buttion. click muxing on the menu and choose copy command line to clip board.
Now in a text editor, paste what you just copied and copy that command out for how ever many episodes you want done now all you need to do is change the file input and output names in each copy to the other episodes. e.g nameep1.mkv to nameep2.mkv
The only problem now is finding a program that will automatically edit the "ep1" in the copies to "ep2" "ep3" and so on. So this doesnt have to be done Manually. Does anyone know of a program that can do this?