When using Nikon "D" lenses on a newer Nikon body that controls aperture from the body you lock the aperture ring on the lens at the narrowest aperture. In the case of the 50mm f/1.8D that would be at f/22.

Be aware that Nikon "D" lenses are normally AF lenses that do not have an autofocus motor in the lens. Nikon AF lenses require a body with an in-camera AF motor to allow use of AF. When used on Nikon bodies with no in-camera AF motor AF lenses must be manually focused. AF-S lenses have focus motors inside the lens and are required to use AF with your D3300.

I want one with manual aperture, but I also want the camera to be able to control it when using presets.

There are only a very few Nikon "D" lenses that are AF-S that would give you both an aperture ring and the ability to autofocus with your D3300. But with "D" lenses you must lock the aperture ring in the narrowest position and use the camera to control the aperture with newer entry level Nikon bodies such as your D3300. Otherwise you will get an "fee" error and the camera won't take a picture. The aperture ring on "D" lenses may only be used to control the aperture with older Nikon bodies that don't allow you to set the aperture from the camera or with newer upper tier Nikon bodies that have a custom menu function that allows you to choose whether to control the aperture from the camera or using the lens ring.