Do we have to build the mobile version separate from the regular version

i built my first site using the mobile template along with ASPRunner 7. I thought that checking the build mobile version option with still build the regular version. But it seems to build only the mobile version when that is checked. When I uncheck that option the the regular version is built. So is it the case where the mobile version has to be compiled separately from the regular version? If so, how does the automatic switch occur?