If the ending key of a song will be different from its starting key, you can easily indicate this in the worship flow.  Just click on the key that is currently set for the song in the worship flow (or the "b/#" icon), then set your starting and ending keys. (If there is not a key already listed for the song, there will be a n/a icon that will achieve the same result.)

You can also specify key modulation for the song in your library (by editing the song).  When it is set for the song in your library, those keys will be used by default when adding the song to any services.