1. Open the PCB editor and select your 3×3 mm pad.
2. In the right-side Properties panel, add or expand the “Pad Size” rule.
3. Set both Width and Height to 5 mm.
4. (If needed) Under “Pad Shape,” ensure you keep the correct shape (e.g. Rectangular).
5. Repeat for any other pads.

• Modifying Pad Size and Shape (Working with PCB Footprints):
  https://docs.flux.ai/flux/tutorials/working-with-footprints
• Generic Footprint Properties (if using a generic part):
  https://docs.flux.ai/flux/tutorials/tutorial-generic-part

You might want to add a hole that's connected to a net. For example, if you want to connect a mounting hole to ground. This is done in the same way as adding a pad with a couple extra steps:

1. On schematic, drag a terminal from the library onto the canvas.
2. Connect the terminal to a net.
3. Switch to PCB.
4. Click on the pad to select it.
5. In the toolbar which shows up above the pad on the canvas, click Pad Type. (Look for the square icon.)
6. Select HOLE.