So for those of us flying on FSE, we have had to modify the CFG to match the FSE fuel tank mapping (FSE only shows a center/Left/Right none of the feeder tanks). So when we start a flight, FSE loads fuel into just those three tanks filling both the left and right first and whatever is leftover to the center....leaving engine 2 with nothing. 

I might have missed this in the manual and I can’t seem to find a good explanation of the fuel system logic when it comes to transferring between tanks, or at the least having engine 2 pull from one of the left/right tanks instead of the center.

Is this even possible? I would assume with the cross flow/transfer valves it should be but I can’t seem to make it work after experimenting with different valve positions etc.

Unfortunately, if you use a third-party program to load the aircraft, it is likely to get it wrong, since the tanks in the 50 are more complex than standard FSX/P3D aircraft.

In normal operations, the left engine is fed only by the left wing tank group, the center engine is fed only by the center tank group, and the right engine is fed only by the right wing tank group.

The cross feeds are only used if there is a problem. For instance, if the left engine has to be shut down in flight, no more fuel will be drawn from the left wing group, so the cross feeds would be configured to send left wing fuel to the center and right tanks to keep the aircraft in balance. If this was not done, the left wing would quickly become heavier than the right wing as the flight progresses.

Each tank group consists of a main tank, and a feeder tank. The feeder tanks supply fuel directly to the engines using electric boost pumps. The main tanks supply the feeder tanks using transfer pumps, which work like a siphon, and use fuel pressure supplied by an engine-driven pump. 

For center-of-gravity reasons, the center feeder tank is larger than than the wing feeders, and the center main tank is smaller than the wing main tanks, but the total amount of fuel in each group (main + feeder) should be about the same at the beginning of a flight. I’ve been working with FSW testing some upcoming updates, and we found that there was actually a bug in the loading for the “light” and “medium” presets in this regard, but that will be corrected soon.

As a flight progresses, the main tanks in the left and right wings and center fuselage will finally empty out, leaving only the fuel in the feeder tanks, which will be down to 600 pounds each at that time. Hopefully, if the flight has been properly planned by the pilots, it will be close to its destination by that time, as the aircraft will have less than 1 hour flying time left when all of the main tank fuel has been consumed.

I assume FSE is FS Economy? It would appear that you should not use FSE to directly load the aircraft fuel unless the FSE developer speaks with the FSW developer to learn how the fuel system needs to be configured. For the moment, you should only load fuel using the FSW-supplied payload manager.