You don't even need the second "boss" group. Just add all your bosses to the main group and any unique bosses you just set to "Don't Auto Spawn". To do that, from the group screen just right click on the unique boss and set him.
WN
Check out one of my most recent arcs:
457506 - A Very Special Episode - An abandoned TV, a missing kid's TV show host and more
416951 - The Ms. Manners Task Force - More wacky villains, Wannabes. things in poor taste
or one of my other arcs including two 2010 Player's Choice Winners and an2009 Official AE Awards Nominee for Best Original Story
Oddly, that option is disabled. 
EDIT: Never mind, found the problem. You have to right click the character in the right-hand panes, not the big list on the left.
Thanks for the help, WN!
I'm trying to get my arc to include a named boss. I want him saved for the end of the arc, and so here's what I've done:
- I have two separate custom villain groups. One group is called "The Tempted", and the other is "Tempted Bosses."
- The named boss is in the "Tempted Bosses" group. He has a unique look and name.
- In the missions, I have set the enemy group to "The Tempted."
- I put a Defeat Boss mission objective in the last mission, and set the enemy to Amron the Damned from the "Tempted Bosses" group.
Here's where things get weird. I see Amron showing up in normal mob groups and patrols as a regular boss. I can't figure out how to exclude him from normal mob groups so that he only shows up in the final encounter. Since defeating him is required to complete the mission, it makes it difficult to figure out which Amron is the one you have to defeat.Any advice?
Thanks!