Alternate Output Text Formatting
Watch the following YouTube video. It walks you thru the options menu and explains how to set text formatting for each of the different types of slides as well as the Alternate Output. That should answer most of your questions. If it doesn't, post back and someone will have some additional information that should help resolve your issue.
The Alt output will only use what is set to the theme it's using. If you edit a song and change something like, italics, underline, color, those are all being set for the main output. The only way it would affect the Alt out is if both the main out and alt out were using the same default theme and when you edit the song, you go to the Master tab and make the changes to the theme.