While using InstallAnywhere, you need to first split your tasks into subtasks. You are packaging multiple products in a single distribution like mysql, weblogic, your application ear file and last but not the least, JRE.
Do you want to support on a single OS or multiple OSes?
Would you be distributing weblogic/mysql setup or exploded folder with configuration UI?
For running a program, it does give you batch file option so you can give that accordingly.
I have used this tool 2-3 years back and it works like a charm. The beauty of it is it supports commandline option and we used to package the distribution using
ant directly from our code repository.
I would suggest you to do some basic reading and then start working on it.
hope this helps.