Hi SB, what an unhappy situation! How old were they? as this sounds a little strange, litter mates will enivitably fight, but this usually calm down given time, maybe it was because they were both boys it was a dominance thing, although I wouldn't expect it to get too nasty at a young age! Did the breeder not offer any advice?
The lone puppy will calm down eventually, you are now experiencing what usually happens when you buy one pup on it's own[although not always, I have been breeding Yorkshire terriers for 4 yearsnow and the owners mostly tell me this has not been a problem]. I would advise that you take away all bedding and wash it, removing all scent of his brother, this is the reverse of what I usually recommend, but if it is stressing him out, it would be better to replace this with something with your scent.....you are his family now. Try to ignore his barking, as if you make a fuss of him when he pines you will be encouraging this behaviour, make lots of fuss when he is quiet instead. That said, let him know he is loved, don't put him in the crate unless you really have to.
Hope this helps, and don't feel too bad, I would also suggest that you find out if your vet offers puppy classes to keep your boy socialised, this will also re-assure your that there isn't anyting wrong with your remaining pups temperament......that sorted....i'd be straight of the local rescue center to find him a companion....lol....but that's just me!!!
Lisa x