Fill only one of multiple selections

Select the shapes. Get a hard-edged brush and paint over each area separately swith the color you want.

Contiguous restrains a fill to a boundery of a different tone.

If you use the paint bucket or Alt backspace with non intersecting selections, it's going to fill all of the selected area.  

That's how it works.  

With the object selected, use the Live Paint Bucket tool. Select a color and click the area you want to fill.