If you want to apply this to ALL RetroArch emulators, edit the retroarch.cfg with this command:
“sudo nano /opt/retropie/configs/all/retroarch.cfg”

Then change
# video_shader_enable = false
to
video_shader_enable = true

And change
# video_shader = “/path/to/shader.{cg,cgp,glsl,glslp}”
to
video_shader = /opt/retropie/emulators/retroarch/shader/hq2x2.glslp

You may also want to consider changing this from
video_smooth = true
to
video_smooth = false

depending on how you want the shader to look.

Make sure you save the file when prompted (press Ctrl-X to exit)

Or you could consider overlays