Since I know nothing about macerator (sp) pumps, I'll guess anyway.
It sounds like the pump has no "lift" capability. Again I'm guessing but it sounds like when you move the hose to a different position, water from the fishbox(s) travels closer to the pump and allows it to draw the water (think prime).
Really decent washdown pumps can draw water vertically about 6' +/-. A standard bilge pump has little or no lift at all. Again, I don't know about your pump but logic dictates it ain't drawin' water
Try changing/shortening the hose run between the boxes and pump. Better yet, suffer the misery and move the pump closer to the boxes (if possible). This will reduce the lift distance and make service easier. You may need to add a new access deck plate.