There are a lot of great options in Creo for making holes. I have my preferred methods of setting up holes.
Drive the hole location with Datum Points or Axis
The way I prefer is to determine where the holes are going to be driven by a sketch using datum points. The added benefit is that doing so makes it much easier to pattern a hole as well as not have to mess with the somewhat clunky placement interface within the hole creation tool.
National Pipe Thread
Select the “Taper Hole” widget. That will allow for the creation of NPT, NPFT and ISO_7/1
Now you can place the hole wherever you want and have all the proper note information associated with the hole.