You can use the version of Management Studio Express. You can download the latest version here - which will work against SQL Express 2005, 2008 and 2008 R2.
If you do not want to install SSMSE, you can use sqlcmd on the command line, for example. something like this (assuming Windows auth and an instance called "SQLEXPRESS"):
sqlcmd -S .\SQLEXPRESS -E -i "C:\path\file.sql"
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