Does anyone know why mercruiser uses two different hose routing, with a mechanical fuel pump they use lower for the inlet and without fuel pump they use the upper port for the inlet . I may have them reversed both of them use the same impeller housing .

I thought it was dependent upon the rotation of the motor, not whether or not it has a fuel pump. That doesn't make sense.

It depends on weather its a vbelt or a serpitine belt set up..the serpitine set up i believe runs backwards so it uses the other inlet..

No, the pumps all spin in a left hand rotation, if the engine is a standard left hand rotation. The reason you see a difference in the inlets and outlets is because the pump is clocked differently. Basically, the pump is rotated over 180*, so what was on the bottom is now on top. It is the same fitting in the same place on the housing, it's just that the housing is turned over.
Eddie

What Eddie said.LH out is always lh out.The pump base where the hoses go can be turned depending on where the 3 through anchor bolts are positioned on the mounting bracket.Left hand rotation (95%) motors use LH out as the water flow out of the pump.

Eddie and fastlane40 are both correct, It's how the pump gets mounted to the bracket, Some guys have in the past mounted the pump on the bracket in the wrong position and then hooked up the water hoses the way they new they came off and had a hard time trying to understand why the new pump would not pump any water.

If by chance it is a RH rotation motor, does it use the opposite port for inlet, or is the pump rotation still the same regardless of LH or RH motor with just a rerouting of the belt in order to maintain a LH pump rotation?

No, a right hand rotation motor uses the port that says RH OUT.I don't believe you can route the belt to make it go left on a right hand rotation motor.
Remember right hand motors are rare.