Ofcourse having 12 subject areas, connected to the same source through different connection pools added some complexity to this task.
Automating 'setting of passwords' the other properties of the connection pool can be done via a command line utility -
admintool.ext /command filename
On conducting some searches, I came across Kumar's blog which has a very detailed step by step process documented.
Here is the link:
http://obieeblog.wordpress.com/2009/08/04/simplifying-migration-process-%e2%80%93-changing-environment-specific-variables-in-rpd/
Anisha