Set the distance or steps per first - do this approximately by calculating the ratio between motor and axis, enter this in tuning, set speed to say 1000mm/min and accel to 100mm/s/s
Next get the distance accurate by using auto calibrate on Mach diagnostic screen (i think) - enter a distance, mach will move, then measure the actual distance it moved and accept the result - use a big distance if you can accurately measure this - a good steel rule or accurate measure is needed, the bigger the distance the better.
Then tune your motor speed, do this by increasing the speed in tuning in steps of say 500mm/min until the motors start skipping when doing a rapid jog - be careful if you have slaved motors or you can rack(twist) your gantry.
each time you increase speed, increase acceleration by 1/10 so if speed is 5000 then acc is 500.
Once it skips, reduce the number by say 20% and try it - if it works well and keeps position then all is well.
Next you try upping the acceleration until it screams at you or loses steps - then back off again.
The two are sort of inter-related but not directly

Eventually you will find a sweet-spot for your machine but once set you should never need to change steps-per unless you alter the drive system.