This is becoming an FAQ so it's time to blog it for the record.

If you want -or have- to manually process the Expression Encoder 2 job output in order to publish the player and video to Silverlight Streaming, here are the three simple steps to follow. The first two are script-able to make it even easier.

First, go to the Expression Encoder output folder (in "C:\Users\<username>\Documents\Expression\Expression Encoder\Output" unless you modified the default configuration), then run this little script in a command prompt to create the manifest.xml you'll need later.

@echo off
echo ^<SilverlightApp^> >manifest.xml
echo ^ ^ ^<version^>1.0^</version^> >>manifest.xml
echo ^ ^ ^<loadFunction^>StartWithParent^</loadFunction^> >>manifest.xml
echo ^ ^ ^<jsOrder^> >>manifest.xml
echo ^ ^ ^ ^ ^<js^>MicrosoftAjax.js^</js^> >>manifest.xml
echo ^ ^ ^ ^ ^<js^>SilverlightControl.js^</js^> >>manifest.xml
echo ^ ^ ^ ^ ^<js^>SilverlightMedia.js^</js^> >>manifest.xml
echo ^ ^ ^ ^ ^<js^>ExpressionPlayer.js^</js^> >>manifest.xml
echo ^ ^ ^ ^ ^<js^>PlayerStrings.js^</js^> >>manifest.xml
echo ^ ^ ^ ^ ^<js^>player.js^</js^> >>manifest.xml
echo ^ ^ ^ ^ ^<js^>StartPlayer.js^</js^> >>manifest.xml
echo ^ ^ ^</jsOrder^> >>manifest.xml
echo ^</SilverlightApp^> >>manifest.xml

Second, create the zip archive as follows:

zip myVideo.zip manifest.xml MicrosoftAjax.js SilverlightControl.js SilverlightMedia.js ExpressionPlayer.js PlayerStrings.js player.js StartPlayer.js *.jpg *.wmv *.xaml

Note that the js files are listed individually on purpose to make sure we do not package Silverlight.js in the lot. However we can use the wild card for the other file types.

Third, go to http://silverlight.live.com, sign in using your Windows Live ID credentials, browse to the "Manage Applications" page, and manually upload the myVideo.zip file to your SLS account.