You will have to build a batch file with more instances of the SJA like described here:
http://webyog.com/faq/27_35_en.html
Once you got one jobfile you can easily generate anotehr by 'search and replace' in a text editor.
A more advance solution is to execute the SJA from within an aplication/a script that does a 'loop'. Inside this loop you will then basically have two statements
1) execute SJA
2) replace in the jobfile