This MSDN article walks you through creating a setup project which installs MSDE and runs a few SQL scripts as part of the installation. Dated March 2004. Involves coding some custom actions.
BTW the MSDE 2000 Deployment Toolkit was developed by chaps at sqljunkies.com even though the article appears on MSDN.
Read more at msdn.microsoft.com/library/default.asp?url=/library/en-us/dnmsde/html/msdedepl.asp
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