How do I ensure my bit will not hit a clamp when traveling across the machine bed?

In the Toolpath tab, select Setup Material and Rapid Gap

In the form that opens, you will find a data entry box for Clearance (Z1), which is also referred to as the Safe Z. This is the height above your Z Zero reference point that the bottom of the bit will rapid at across the machine bed.

  Z1-Z2

If you are using clamps or have another need for the bit to travel above a certain height, this value is what you will set to control that.