My Sparkler's safe place is under the bed too. For the longest time, she only came just out to eat (and I assume to use the litterbox, though I never saw her do it). Then she got an infection and started hiding inside the bedsprings box! I finally managed to get her out far enough so I could grab her and take her to the vet's for an antibiotic shot.
Sparkler was severely traumatized when she was a young kitten (stepped on and her hind legs crushed), and I think that is the source of her timidity. Murphy probably had a very frightening time of it as a young kitten in a feral colony, so he learned to be very fearful and defensive too.
I started luring her out with food and then reaching to wherever I could reach her to pet her and give her lots of affection and attention. The infection cleared up, and she started coming farther out.
Now she comes out a lot, into the living room even! I can reach down and pet her and give her something to eat. And while under the bed is still her safe place, she comes up ON the bed when I lay down to go to sleep so I can pet her as we both drift off!
So please give your dear Murphy whatever time and space he needs, and give him loads of affection and attention (plus yummies!) when he does come out. He and Nugget will work out their interPURRRsonal dynamics. How cool that is that they bump noses and even sleep on the bed together with you at night!
I meant," said Ipslore bitterly, "what is there in this world that truly makes living worthwhile?"
Death thought about it.
"Cats," he said eventually. "Cats are nice."
-- Terry Pratchett, Sourcery