Sure, you can choose between -d and -D, the only difference is that -d is better if you have many files in sub-sub-directories so in general -D is the way.
-d automatically create an additional output folder with the name of the
input folder and file processed, eg. models/mychar/mychar.arc/*,
-d works also if input and output folders are the same (rename folder)
-D like -d but without the folder with the filename, eg. models/mychar/*
You can set the option in a .bat or in a shortcut link to quickbms.exe or via command-line.
Probably it also works as argument of the quickbmsver instruction in the script.