The way i think of it is, the Acceleration and Velocity settings in Mach act like your speed limiter, they over-ride whatever settings the CAM software specifies in the job.

Its also critical (although I cannot explain why) to ensure the Acceleration and Velocity settings are the same for both your Y axis and X axis. (Z can be different) Otherwise (I found) it effects 90deg corners. Where (I think) the machine is still decelerating (moving) when the next move starts

Personally (others will disagree, I set the accelleration very low (often 100), and the velocity to a comfortable speed for the machine as Im far more interested in quality, than speed) I also find having acceleration set so low helps when jogging your machine manually into a start position and also makes a nice smooth start and stop to each move.

As mentioned above, Mach is your speed limit. So if you have set your velocity to 6000mm/min in mach, and your tool to 8000mm/min in vectric (or your cam software) mach wont let the machine exceed 6000.

The machine jogs (ie with the arrow keys, at the maximum speed stated in mach)
The machine moves (between cuts, at whatever speed the Gcode outputted by your cam software) -- but limited by mach.

The above is just my opinion.