Once you create a project with Sitefinity project manager, you can simply copy it to any location you desire (e.g. to the Default Website so that you don't have the virtual directory as part of your urls). It works in the same way as you would transfer the finished site to the production server.
Project Manager in Sitefinity is just a tool that automates certain tasks for you - but it is not connected with the actual Sitefinity site - so moving the project won't cause any problems.
I hope you'll find this information helpful. Let us know if there is anything else we can do for you.
the Telerik team
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