You can buy all the components you need at radio shack and make your own. I did that one year, but by the time I finished, I realized that I could have paid less buying a bunch of eye sets on ebay (those makers buy in volume and pay much less than radio shack prices), and save using single shipping for the multiple sets. The colors were better and more varied too.
Assuming you have a pair of wired LEDs available, there are several ways to install the "eyes" and much depends on the subject waiting to be illuminated.
If the subject prop already has eyes, many people just poke a hole in them and glue the LEDs from the back side. Although this works perfectly fine, you might find that the brightness of the LED is too severe for your setting. I have used red LEDs placed on cardboard behind the eyesocket and then a scrap of nylon fabric - red or black - stretched over the opening of each eye. This will disburse the light a bit, making it less intense and, IMO, a more "real" than just the bare bulb. This works great with full head masks that you are utilizing as components of yard monsters.
You can do the same thing with skulls very easily. We have also tried costume jewery as a lens in front of the LED. This can be fun too, sending the light in varied directs dependent upon the "cut of the stone."
This year ... see my album ... we chose not to cover the LEDs of our outside ghosts because they are up in the air, at a distance. I might use white nylon fabric over them next year.
One more tip. Because our ghost's eyes were so far up in the air, and because I'm basically lazy and cheap, I didn't want to mess with batteries for them. So I used a couple of Malibu light transformer sitting around in my garage to power four ghost's eyes on one side of my driveway and another to power three on the other side. These were lit for 6-8 hours every night for about four weeks and no LEDs were burned out.