Boondocker is setting up their fuel system differently than the other turbo builders. They are using the stock fuel pump circuit and adding additional voltage and amperage to it by pulling additional power from the lighting coil and adding it to the fuel pump circuit. This is keeping the load on the stator balanced b/c all coils are being used. Often fuel systems are run so they start on the stock fuel pump coil then use a relay to switch to the lighting coil where additional amperage is available. This leaves the stock fuel pump coil with no load while the sled is running, unless you add something like EGTs, Aux injectors or and A/F gauge to that coil.
Back to the boosting the fuel pump/fuel pump circuit. This is done through the fuel booster board. On the booster board you have a high voltage side that is pushing 21ish VDC out to the pump. The board is proprietary so I don't know the details of how it's done but I know higher voltage is being used and creating a Variable DC drive of sorts. If the OP is replacing his pump, and using the booster board, then he must be running a 08 or older M1000. The replacement pump isn't necessary on the 09+.
To the OP, I believe you are going to need to switch the polarity on the wiring in the tank going to the pump. You need to contact BD and get some clarification on what exactly you have and how they want you to hook it up.
