I think my 1 year old has a milk allergy. He is extremely fussy for two weeks since switching from soy formula. Runny nose and watery eyes. What to do?

Switch back. Switch back to soy formula as if this is milk allergy the symptoms should resolve. You should have your child evaluated by an allergist to confirm whether or not your baby really has a milk allergy or some other unrelated problem.
Milk allergy. Stop the milk and if the symptoms clear, after fewc weeks give the milk again and if the child gets the same symptoms, that is confirming your suspicion.