A script is probably the best way. Start with an export file from the router you want to use as you master configuration. To simplify things you can trim out anything which you don't care about (for example is you're not using bgp or ospf you can leave those out) or anything you've left at the default settings. Next change adds to sets where you know default configuration already exists (I took an export of the default router configuration and use it as a basis of comparison) in some cases (like firewall rules or logging) you may need to do some removes first. This may sound complicated, but it's mostly just simple transformations given an export file, and once it's done you can reset the router to defaults and reconfigure it within a couple minutes if you ever get in trouble.
This posting discusses the types of transformations needed:
http://forum.mikrotik.com/viewtopic.php ... et#p281134
There are also a number of example setup scripts on the wiki which you can use for reference. This is just a sample:
http://wiki.mikrotik.com/wiki/A_script_ ... ou_started
http://wiki.mikrotik.com/wiki/How_to_Co ... _xDSL_Line
Also see this utility: http://forum.mikrotik.com/viewtopic.php?f=2&t=40092