I have had the Yamaha Fuel Management System on my boat since new (1994). It is still acurate to within a gallon or two. I carry 216 gallons but rarely let it get down too far. Anyway, I don't see what difference two pumps would make. If you are talking about fuel pumps on the motor, on my old 2-stroke, there were six. The sender goes into the fuel line. All the fuel would flow thru the sender before it gets to anything that may affect it.
In my opinion, the fuel management system (flow scan) is a very valuable tool. As Fishraiser said, you can tell your optimum cruising speed for maximum fuel economy.
Joe