Generally you have a Default website under your IIS server. Under this website you can run Sitefinity as new application but your Sitefinity projects will be recognized as directories of the main domain.
Default website - domain.com
- new ApplicationOne - domain.com/ ApplicationOne
- new ApplicationTwo - domain.com/ApplicationTwo
Another option is adding a new website for each Sitefinity installation
All the best,
the Telerik team