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.

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.