If IIS is working you should be able to open an IE window and enter
https://localhost and get something other then page cannot be found, to see if IIS is working.
I saw a simular message to your's while trying to install eManager on a Windows Server 2003. I gave up and installed it on a different machine. Win 2003 is not supported.
They say that only Win XP is supported, but I have seen eManager running on WIn2K a few times before.
I know you have had problems installing emanager before. Not sure if you tried to re-install IIS yet, but definately worth a shot.