The Gemini Wizard will setup the number of counts per electrical pitch by the encoder resolution. If you look at the full setup Wizard, the pitch distance is the equivalent of 1 rev. Looking at the 404LXR...E2, it's 42mm for the pitch and 1um resolution, 42000 counts will move 42mm.
If you select Trapezoid for your Profile, your distance is in encoder counts. Continuing this example, 42000 counts would be a 42mm move.
The velocity and acceleration corresponds to pitch/sec and pitch/sec2, so 0.5 rev/sec setting would be 21mm/sec (0.5 * 42000 counts/pitch = 21000counts/sec = 21mm/sec) . If you were to set the maximum acceleration to 5 rev/sec^2 this would be 5 pitch/sec^2 * 42mm/pitch = 210mm/sec^2 linear acceleration.