First of all, JACAL is very raw. It is currently tuned to the needs of the Taylor University CSS department. There are hard coded machine and path names in the scripts and things like that. Eventually these will be stored in a configuration file and there will be an install script to assist you in using this stuff, but until then...
Read through the documents in the docs directory. You will be confused. Make notes on things you are confused about and how the documentation could be better and better organized. Keep these notes to send them to us so we can update them.