Lori had a great suggestion about putting the boys in a room so they can't get at Samantha. She will come up if they aren't there to chase her back down.

I'm finding that things go real smooth when both cats are sleeping because Peanut sleeps upstairs and CJ sleeps downstairs. It's almost like Peanut forgets he's there. She's her old self....until he decides to come upstairs. Then she goes on the defensive until he goes back downstairs. So as long as Samantha knows she can roam freely without the boys being right around the corner, she will come around.

It think this will also help because it will get her scent all over the house so the boys can get used to her scent being in all their normal places.

Good luck and hopefully things will calm down soon. I'm in the same boat as you right now in trying to introduce a new kitty - what fun, eh?