If you are encoding multiple bit rate versions to one ismv file, which you can do with Expression 4 Encoder, that won't work in Wowza. They need to be separate files.
We really don't recommend this encoding path using Expression 4 Encoder. It can work, but the .ismv files are fragmented mp4 files and incur substantial added overhead, especially right at the beginning of client playback.
Take a look at this guide to encoding vod content, which includes pre-sets for E4E