Hello Ceonie,
I don't know whether the synscan hand controller and the Eqmod interface values need to be the same. I suspect not, but you might want to ask on the EQMOD forum.
PHD2 will usually work best with a guide speed between 0.5x and 1.0x sidereal rate. The exact value is not important since PHD2's calibration will figure out the actual rates. Personally I would set the rates on both axes to the same value to keep things simple, but it is not required that the rates be the same, and PHD2 makes no assumptions about the rates being the same.
Andy