For parts with a clear pin numbering scheme, pin 1 is usually given a square pad to tell it apart from the other round pads.
If you'd like to have the pin numbers included on the overlay, then simply add them on the overlay in the footprint of the part. This information will then automatically be transferred to the overlay of the PCB, too. One drawback of this approach is that the text is static, you can't rotate it in the PCB editor. This causes text to be oriented apparently "randomly" when you rotate parts to fit the layout optimally.