I'm sure you know about the "copy running-config startup-config" command used to save your configuration. However, not too many people know about the command to restore your configuration back to the startup configuration after the router is running. No, the "copy start run" command won't do it. That just merges the startup configuration with the running configuration.
Since IOS 12.3(7)T, a new command has been implemented into the IOS: the "configure replace" command. This command will allow you to truly replace the running configuration with the startup configuration, just as if you had rebooted the router.
There are many variations of this command, but my favorite is the "configure replace nvram:startup-config list" command. This will replace your current running configuration with the startup-config file located in NVRAM and list the commands that were removed/changed.
Hope this will help :-)