What boundary should I be using for a cleanroom if my inlet and outlet velocity are at 0.4m/s. But the inlet and outlet dimensions or area are different.

Are you saying that you don't have mass-conservation in your cleanroom? Having the same inlet and outlet velocities but different areas implies this unphysical conclusion.

If I have o.4m/s velocity as inlet what boundary condition should I be using. I mean the bondaries condition for the inlet and outlet for the cleanroom having different area for the inlet & outlet.

I'd use a velocity inlet and a pressure outlet. Set the outlet pressure to the ambient atmospheric pressure. When you have a solution you should check that you have mass conservation, ie that the mass-flux in equals the mass-flux out.

What about the operating condition, do I have to set anything there?? And for the inlet and outlet temperature, do I remain it as default at 300k??

The operating condition is just a "base pressure". All pressures you give as boundary conditions are relative to this operating pressure. If you set the operating pressure to atmospheric pressure then you should set outlet gauge pressure to zero in order to obtain atmospheric pressure at the outlet. Set inlet temperature to whatever you think it is. 300K sounds resonable. Outlet temperature will not make much difference. Set it to 300K also.

If the outlet is set as pressure outlet at atmospheric pressure, that mean the outlet is not in suction action. How can I create it as a exhaust fan or at what pressure should I set at.