I'd just fill 'em with silicone, but that might not look all that pretty.
Most hardware stores and electrical supply places sell nice plastic grommets and plugs that are designed to be used with electrical boxes.. if you want it to look pretty, just drill your extra holes out to 3/4" and pop in the plugs.
If in the future you need to use one of the holes, just pop out the plug, pop in a gromet, and use the nice hole.
They're paintable, removable, and look nice.. but won't do any good for large 1" holes.
