By default, the user name and password of the OnBase service account are stored in the Hyland.FullText.Server.exe.config file in plain text. Although these credentials cannot be used to log on to any OnBase client application, you should encrypt these values in the Windows registry using the aspnet_setreg utility.Full-Text Search can then be configured to refer to the encrypted registry keys to retrieve the user name and password of the OnBase service account.
Full details on creating encrypted account registry keys are available from Microsoft. See for example the Microsoft Support article, How to use the ASP.NET utility to encrypt credentials and session state connection strings available at http://support.microsoft.com/kb/329290/.