Yeah, I had this problem too. At the end of the latest Arc I've been working on, I wanted to have Rularuu bosses spawn in my custom group. Alas, it seems the only way to do it currently is to have the bosses themselves spawn from the original groups, or to have the bosses be the only enemies in the group.
You can add creatures from base enemy groups to your custom groups. Just go to the Group Editor, select the option to display All Characters, click on the Nictus group from the dropdown box, and then double click to add the things you want to your custom group boxes on the right.
I heard that it might not be possible to put in base bosses from custom groups, though. I haven't tested it myself so it's something you'll likely have to fiddle with.
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You can add creatures from base enemy groups to your custom groups. Just go to the Group Editor, select the option to display All Characters, click on the Nictus group from the dropdown box, and then double click to add the things you want to your custom group boxes on the right.
I heard that it might not be possible to put in base bosses from custom groups, though. I haven't tested it myself so it's something you'll likely have to fiddle with.
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That first part is exactly what I have done so far, and that works flawlessly as far as I can tell.
Its that second bit that gets me... Phooey. 
Sorry, as far as I know bosses (and allies?) can only show up from their original factions.
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Much like Vermain said you can add to custom groups, however to build on that, you can in fact create a separate custom group just with these in it and save them to another file named Nictus Leadership or some such thing and then force them into the spots you need them for. Often times I will provide certain bosses their own custom group to really distinguish this particular incident as something unusual. You could have them defending an object or holding a captive or even spawn them as your ambush, so you don't have to contend with other mob spawns. Hope this makes sense. 
Xara
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Thanks for all the help folks, I appreciate it. Looks like I will have to do some more experimentation... *makes evil finger steeple*
Okay, I am trying to make a custom group that uses White Dwarves and Bright Novae as its bosses. However, I don't find either in the dropdown menu of my custom group for the purposes of a Boss Fight. I could choose their parent group (Nictus) but then I won't have the custom group's name listed as the Faction (not to mention that I would then have to set the Surrounding Group to Custom, if I can even do that, I haven't checked).
Help?