Virtual IE comes with default settings that are suitable for most circumstances. However, by editing the ldf that were used to create the virtual application, you can customize IE to meet your specific requirements. The ldf is an xml file. It contains the definitions for all files, folders, file system Access Control Lists, and registry settings that are required to create a virtual application. All of the IE settings are customized by editing registry settings.
The "How to configure Virtual Internet Explorer Settings" article on Symantec Connect provides details on customizing IE.