Yes they will know the difference b/c not only will you test positive for amphetamines, but they can break it down to which drug was used. Adderall and meth have different metabolites.. So with further testing, they can tell the difference.
It also depends on the test itself. Now if its a urine test yes they can break it down and find out. But if its a hair follicle test it will just show up positive for amphetamines. If you have a prescription for lets say ritalin then you should be ok.