Is the area now grass? I think once you dig up and prep the area where you plan to plant the trees and veggies then she will find another place to do her business.

But, if you want to train her to another area, then I'd vote for grass. You may not even need a fence. I would mark the area with flags, then remove them once she starts using it regularly. Be sure to use some of her feces to mark the new area.

I'm bagging dog poo and moving it to less obtrusive places. Is there a more eco way to handle it? I do like the idea of having my 5 mo old puppy use one area..... then I don't have to "sweep" the entire yard!