At the simplest level you can create a batch file to run your sql scripts.
Something like:
cd "C:\Program Files\Microsoft SQL Server\100\Tools\Binn"
SQLCMD -E -S .\SQLExpress2008 -i "E:\SQLExpress 2008\Publishers\InstPubs.sql" -o "E:\SQLExpress 2008\Publishers\InstPubs.rpt"
Look up
SQLCMD[
^] here.
You can write a PowerShell script to do it
as here[
^]
You can use SSMS (Sql Server Management Studio) to schedule a job:
as here[
^]
Or you can write an application in the language of your choice to do it for you.