Best way to add external power supply when main PSU is a solar charge controller?
Should I power the Arduino with the buck converter parallel to the same PSU (the 12V 20A Solar Charge Controller) I'm using for the pumps

Yes. However I wouldn't use a 9V buck regulator, but a 5V one and feed it to the 5V pin. That way you bypass the wasteful LDO on the Arduino, and when running from solar every bit of power saving you can muster helps.

and is it safe that way?

Yes, it's safe. As long as the buck regulator you are using is rated for the voltages in question.