Which way to hook up boostrap diode for switching regulator?
The anode of the diode is not shown connected anywhere. You can connect it to either the IN or OUT (obviously if you connect it nowhere you can omit the diode). 

The cathode always goes to BST if the diode is present. 

The purpose of this diode is to charge C23 when the output switch line (SW) is near to ground. Since the internal MOSFETs are n-channel the gate voltage must be higher than the source voltage in order to turn the MOSFETs on. 

Since your input voltage can be higher than 5.5V you have two options only- leave the diode out or connect it to your 5.0V output.