Make a copy of your whole vanilla RTW folder and label as Roma Surrectum - now install the mod in here.

The problem you've got relates to not allowing the batch file run itself in its entirety. You've got to let it run (obviously responding where appropriate with A - all - when indicated).

I'd recommend checking out the twcenter site where most issues are dealt with and help is more readily at hand...

http://www.twcenter.net/forums/forumdisplay.php?f=251