My very fisrt suggestion is to ALWAYS feed them separately. This will help your other pup not feel so "bullied" also. If the only tension is around food it sounds like he has a touch of food aggression. Doing things like pinning him can actually make this worse so I think you are doing the right thing by giving him a time out. Something else you could consider is filling a squirt bottle with water and spraying him when you hear the first growl. This will stop it and then you can give him a correction immediately so he knows right away what he is doing wrong.