For the condition of replicating the boundary layer transition over an airfoil, I have meshed two separate zones in Gambit, such that the condition of laminar flow can be applied for a specific domain, after which turbulent condition takes over as the flow moves aft towards the trailing edge. I am not sure where exactly in fluent the condition of laminar and turbulent flow can be applied independently for each zone. I have tried the boundary condition menu, but with no luck. Any advice?

Try "define/boundary conditions/fluid" and check "laminar zone" option (that of course only for the laminar portion of the airfoil).