Poor baby.
The most important thing is to not let the scab close because that will allow the infection to continue to come back. Make sure to flush it out several times a day.
I agree, that you need to ask your vet for clavomox, it is the best stuff out there for skin issues.
Also, if you are still having issues holding him, try to Burrito Method... aka wrap the rat in a towel snugly to restrict his motion. This method has worked very well for me with a variety of squirming animals.
Best of luck.