Do we treat schizoaffective different than bipolar?

Somtimes. As both involve mood changes, mood stabilzers are commonly used for both conditions. Antipsychotic medications are required for the psychosis as it related to schizoaffective d/o. Such medications may or may not also be a part of a patient's regimen for bipolar d/o.
Sometimes. Individuals who suffer from schizoaffective disorder often need more help addressing their symptoms of psychosis, like hallucinations or delusions. Individuals who suffer from bipolar disorder experience psychotic symptoms only during a mood episode, and often do not need help to treat psychosis when their mood is under control. However, in general the medications used are the same.