You can easily setup two limit switches(home and limit for example) using 2 of the DIN I/O pins per motor. Setup can be done through the Ion Motion setup application. Each pin can have a min and.or max action setting. The levels at which the actions trigger are also programmable.
In the ion motion software select the DIN pin you will use for an action(for a Limit in this example). If the limit will trigger when pulled low, set the Min Action to the specific Limiting action(M# Forward Limit or M# Reverse Limit). Then set the Min setting to 2048. This will set the trigger voltage at approx 2.5v. if you want a lower trigger point lower the Min setting.
For homing(where the home switch also acts like a limit switch) you want to set both a Min and Max action. In a case where the Home switch is active low set the Min action like a Limit and the Min setting to around 2048(or lower) as with the Limit switch. Then set a Max action of LoadHome and set the LoadHome value to the home position(usually 0). Then set the Max setting to 2048 or greater. When the home switch is triggered(goes low) the motor will be stopped(because of the limit function). Then when the motor is moved out of the home sensor the LoadHome function will execute giving a precise home position at the switch trigger point.
Note this is only one example of how homing can be done. There are many different ways to configure homing(foward, backward, forward with an offset, backwards with an offset etc...).