Some games also may just be incompatible with newer Amigas, and should be run on an (emulated) A500.

There are some pre-made configs in E-UAE's Conf directory and if you look into Bonus directory, you'll see some stuff how to integrate E-UAE into Ambient's context menus. I'd suggest that you'd install them and then you can run ADF:s from Ambient by right clicking them. There will be an option to run them in A500 mode, which is good for the most disk based games.

I'd only run your own HD installed setup for other than ADF stuff.