The breakdown of these stages goes something like this:
The stepper is most likely a 1.8 deg/step standard type. The encoder will have XXX pulses/revolution and is connected to a second shaft coming directly from the motor. While the stage has a 2mm pitch (2mm travel/revolution of screw), this gives XXX pulses pre 2mm of travel. There is probably a gearing ratio, most likely a worm gear. Worms ratios are usaully in the range of 20:1 to 100:1, giving a XXX*100pulses/(2mm travel). With the 2nm/ pulse reported by the stage supplier, and assumin a 100:1 gear ratio, the encoder has XXX=10^4 pulses/rev. This is incredibly high. I have never heard of anything higher than 2000 pulses/rev.
I suggest contacting the supplier and asking for specs on the encoder itself, which will be reported in pulses/count ( or counts/rev), not in length/pulse. This is the number you specify in MAX.
For the steps/rev:
MAX will read the microstep setting set on the 7604 and will assume a standard 1.8 deg stepper, which is 200step/rev. So, if you set the microstep on the 7604 to 10x, the 7344 controller will read 10*200=2000 steps/rev. Now, if you want to include gear ratios, you must manually multiply it in MAX. Normally, this is not done, since max velocities are specifed at the motor. If you use a rotation stage, then you might want to multiply it in. It's a matter of taste.