You mean In code?
mojoBasePage and SiteModuleControl base classes have a property SiteRoot which will correctly resolve the folder name of the current site so the link would be SiteRoot + "/mypage.aspx";
There is also a function SiteUtils.GetNavigationRoot() that will return the correct site root including visrutal folder name for the current site.
Note that its only the pages that need to use the virtual folder path as part of the url, images, script etc must still use the actual site root like WebUtils.GetSiteRoot() or in mojoBasePage and SiteModuleControl we have property ImageSiteRoot
Or a fully qualified link will always work for pages. http://mydomain/mysite/mypage.aspx