Several different ways to cover up un-used holes......including all that are already listed.
1. Quick and easy........put a bolt in the smaller holes.
2. Also quick and easy.........if you are not going stock. Install a switch, gauge cig lighter or another dash light in the holes. If you are making modifications anyway, chances are you are going to need one or the other. Bolt on a cup holder. Go BUBBA CRAZY!
3. For filling larger holes smooth.....I like to make a bigger hole to start with. To do this you need a metal hole saw bigger than your current holes. If you currently have an 1" hole, get a 1 1/4" or 1 1/2" hole saw and cut your hole to that size. Then, take the same hole saw to some spare metal and cut a plug out the same size to use for your patch. Presto! Your patch should fit your hole very closely and just leave enough gap to weld around. Take your time welding and grinding smooth with plenty of breaks to avoid heating the metal up too much and warping it. You should also weld in the plug using a criss-cross pattern to keep it flush in the hole.
Good luck!