Hey there so as @Simplicity mentioned, Photoshop works in layers and this is some of the fundamentals of the program.
I wanted to clarify the answer though for people in future.
Firstly here are some pointers on layer basics which is a good place if you are just starting.
Secondly in this particular example the problem is that the OP is experiencing some issues because the black fill using the paint bucket tool (G) is not aligning smoothly with the edges of the white ellipse. This is an ideal example as to why layers should be used in Photoshop.
To over come this problem you simply use a layer that is entirely black placed beneath a layer that is transparent except for the white ellipses.
Here you can see the arrangement of the layers and the effect that it has on the ellipses. As you can see there is a smooth edge because the black fill actually continues beneath the white ellipse so there are no pixels left blank. Arrow 1 is pointing at the icon used to make a new layer, alternatively you can navigate to Layer > New > Layer or use the shortcut SHIFT + CTRL + N