In case you want to do it manually: you need two sketches, one for the small holes going through all, one for the bigger counterbore with the appropriate depth. You can reuse your Sketch001 for the former and Sketch002 for the latter, where you have to remove the not used circles.
here is an example. Remember to select 'Reverse: true' for the pocket menu when the pocket is selected
in the Model sub-window properties.
Update: Please reference the attached tutorial on using the Polar Array tool from the Lattice2 workbench. If you're performing multiple
cuts from the same object, the Lattice2 workbench really comes in handy. What is great about the Polar Array tool is that you can define the number of array elements as well as their angular and physical distance from the center.
I confirm the 2 answers above: Hole does not work with a non-flat or non-parallel base surface
Note that here, DatumPlan is useless for the 1st: you draw the sketch of the holes on the XY plane, and
for the counterbore also by modifying "Attachment at the right height
for my answer, I keep your 1st and its DatumPlan, I transform the 4 large diameters into construction lines (in blue) so as not to redo everything and Pocket "througt all"
and for the big ones, I make a carbon copy, swap the circles and move the bottom of the holes to the right place with "Attachment"