Application Page: After deploying Application page, it will move to sharepoint server. The path is: Hive\Template\Layouts\15\<ProjectName>
ASCX: After deploying User control, it will move to sharepoint server. The path is: Hive\Template\Layouts\15\controltemplates\<ProjectName>
In both cases, server side code will build as DLL and deployed in to GAC.
When project adds DLL in GAC, then SharePoint requires Apppool recycle.