Jack Russell Terrier and his Aggression

I have a 2 year old Jack Russell who has worn me out( at least thats how it feels) with his big headed aggression issues. When i first got him up until he made a year he was so loving( towards other animals, cats and dogs), and did not show aggression towards other dogs. It seems that literally after his 1 year birthday he got into his first fight with my Australian Yorkshire Terrier( both terrier= bad). Ever since then he can not..no longer... play or socialize with another dog unless he has a muzzle on...even with that after a little while he will try to snap. He knows his basic commands...after a LONG time of training, and has improved some what with the training we have been getting him, but his aggression is now and has been my biggest and main concern. Im happy with the trainers that have really help me and him learn his basic commands, but I do not know what to do when it comes to socializing with dogs he has 1) grown up with since he was a puppy 2) bigger dogs( new friends) and 3) a new 8.5 week old puppy my boyfriend has just adopted. He has good days and bad days. We have walked him and the puppy together( he had his muzzle on) and he did well up until the point when they came to a stop, with out it he would have tried to eat the poor pup! They have had short introductions most have gone well, we make sure that they both received a reward and praise when they have a good introduction. I know that before long this baby German Shepherd will be MUCH bigger then my JRT and sooner or later he will not be ALPHA over the shepherd, but i do not know what more to do about this prolonged aggression. Advice from anyone with similar experience is very much appreciated.