It really doesn't make any difference. Because of the pressure drop across the IC and the TB, manifold pressure will always be a little lower then pressure at the turbo outlet, but regardless of where you take the signal from, its going to be whatever you set it at.
If you want 15 psi manifold pressure, and your boost gauge is connected to a manifold source, you simply adjust the MBC your boost pressure, as measured by the gauge, is 15.
BTW, the OEM system takes the signal from the turbo outlet.
bill