You can sight from the rear of the fuselage and be fairly accurate.
I put an ink line centered through the wing cutout on both fuselage sides before installing the wing. I then make sure my flap fillets are centered on this line when I install them. After the model is finished and I am ready to install the flaps I just align them with the flap fillets and I know they are even.
If I forget to mark the fuselage before I install the wing, I level the wing on my work bench and use a height gauge I made with a pen to mark the fuselage sides.