I've not used Exmerge in an application that would run every night - if you're just trying to syncronize two servers in different Exchange organizations, the Interorg Replication Utility would seem more appropriate.
However, a batch file would look something like this:
net stop MSExchangeIS exmerge [whatever command line parameters are needed] net start MSExchangeIS
This batch file could then be called by the Task Scheduler so it would run every night.
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Exmerge
Thanks for your help