With a Baja car I'd want the punp up quite high to give all the protection it can get.
You need a swirl/surge/supplementary tank (the same thing but different names) to supply the EFI pump.
You need to run a line from the fuel cell to a "lift" pump, this can be a carby electric pump (Carter make a nice one and so does Holley) which pumps the fuel to a holding tank of less than a gallon, it can be bigger if you wish. This tank can be mounted in the tray out of harms way above the fuel cell.
The fuel is then pumped from the bottom of that tank with the EFI pump to the engine. This ensures the EFI pumnp always has fuel above it.
The fuel return from the engine goes to the supplementary tank.
You need an overflow from the supplementary tank to the fuel cell.
Google swirl pot (or simillar and you'll find good diagramatics of the above.
Just remember the fuel into the supp tank goes in high, the engine return goes in high and the overflow comes out even higher.
The fuel to the engine comes out the very bottom.