Thank you for using our services.
There should not be references to the parent directory your website is created, if you are using relative links with ~ notation. The ~ would resolve urls to the root path of your website. For example if you have added user controls to your toolbox in the web.config the property would be set as url="~/pathtousercontrol". Also by default Sitefinity does use dynamic links so links on your site should not break too since paths should be automatically resolved. If you have added references to other projects when you need to move to the new development environment you might need to fix the reference paths so that your project finds those references. You might need to fix the connection string to you database since you will be moving to a different environment you would probably use a different DB server for your DB.
You can test this by simply creating the sample Telerik University site from Project Manager. Then copy the website created in Sitefinity3.6\WebSites folder to an arbitrary location. Go to IIS select add new application and add the just copied website. You will see that the website will run as it should.
If you have any particular references to the Sitefinity3.6 folder could you, please tells what are those references. This will help us come up with some suggestions on how to fix them when moving to different environments.
All the best,
the Telerik team