I currently have a stand alone instance of Youtrack 6 installed from the ZIP distribution.
When I try to import the database from the Youtrack 5 instance into Youtrack 6, Youtrack 6 starts up using the host and port of Youtrack 5, which is a WAR file running on Tomcat.
ie. My Youtrack 5 instance could be access at <server>:8080/youtrack, and I setup my Youtrack 6 instance to run on <server>:8081. After importing the database, all visits to <server>:8081 is immediately directed to <server>:8080/youtrack.
I followed these steps to import the database from Youtrack 5 to Youtrack 6.
Database left baseURL without changes. Please, restart YouTrack 6 instance with following parameter: jetbrains.youtrack.baseUrl
Refer to https://confluence.jetbrains.com/display/YTD6/Providing+Java+Start+Parameters to learn how to provide Java parameters directly for ZIP and MSI distributives.