Hi Yair,
The Overshoot.pde is intended to test the reaction of the library to the case where the target position is changed while the stepper is already tracking to more distant target position. IN this case the stepper will have to slow down and reverse direction mto achive the new target.
Analog pins: Ummm, dont think so?
Re limit switches and interrupts
prob it all depends on the cycle time of your polling loop and the max speed of the steppers. Need to be sure you have enough time prevent the next step after the limit switch is tripped.
Cheers.