You may also consider using SMSInstaller (downloadable from MS) or the Winstall Lite. Winstall Lite is on the Windows 2000 Server CD in the ValueAdd folder. You can use these to create pre-packaged versions of the applications, so that they can be configured to install correctly no matter who is logged in.
In addition, you can use Active Directory to deploy the applications via Group Policies. Here is MS Knowledge base article Q257718 that outlines the process nicely: HOW TO: Create Third-Party Microsoft Installer Package (MSI)
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