If it's wood, just outright replace it.
If it's metal, I've had success with using
J-B Weld to attach a small plate of metal behind the hole, letting the J-B Weld cure. Then fill in the hole on top with more J-B and waiting just long enough to cure to work with but not so long that it turns its hardest. Ive only done this to fill in one or two holes here and there.
I know people do the same technique I explained above using wood (as you did) instead of metal as a backing (for me it works best with "flat" panels, I don't have too much incentive to "shape" wood on curves), spot welding new plates and using bondo instead of J-B. Don't use wood putty, it doesn't seem to stick well to metal, shrinks and is relatively soft.
I really like the look of metal panels but don't really invest a lot into their repair. So if there are too many holes I would say just take it to a local metal shop to have them bend/shape you a new one.
