You are able to use your saved Input Specificiations when running in Batch Mode. This allows you to create a custom Input Specs file while using the program that you can use over and over again in Batch Mode.
The basic syntax for using the Saved Input Specs in batch mode is as follows
/I=inputspecsfilename
You can also override the directory entered in the Input Specs file by specifying the /D parameter in the Batch Mode parameters. An example of this would be
Disk Triage.exe /B /I=LanShare_HomeDirs.inp /D=x:\public
The above line would run Disk Triage using all the settings from the input file - but overriding which directory was being sized - making it use X:\public directory.