In your part of Virginia, I don't know what your projections are for how hard you will get hit and what is supposed to hit you. If the current computer models hold, you'll be on the dry side, but with that cold front that went through here coming your way, who knows what will happen where you are. Normally with the track of Sandy I'd think you are not going to have it too bad, but that cold front makes it even more unpredictable. These things are unpredictable to start with, though they are getting a lot better at it. I lived on the Gulf Coast for over thirty years so I've seen a bunch of these, just not with that strong cold front hitting it.
What you need to do depends a lot on what you are projected to see. If you are right on the coast, your tides and the storm surge will be pretty high until it passes to your north, then the counterclockwise winds will draw the water out. With these things the storm surge is the thing I worry about the most. With the current track, the people I really worry about from this are those in New Jersey and further up, especially those right on the coast. If you are not on the coast, this is not a problem for you. If you are where this can be a problem, they should tell you to evacuate.
The next problem is rainfall and the risk to you and your chickens really depends on your local conditions. You are on the dry side, but with that cold front you might still see a lot of rain. With hurricanes, those usually come in bands, real heavy rainfall for a while then it slows down of even stops, and then another band will come by. The risks here are flash floods if you live in hilly country where the water can concentrate and get real deep and fast real fast. Virginia has a lot of that kind of country, but where you are located has a lot to do with whether that is a risk for you. The other problem is that you night be in a low-lying area where the water will drain to and form a lake. Sandy seems to be slowing down, which is not good. The slower it is the longer it has to dump rain on one place. If flash floods or water building up in low lying areas are your problems, the only thing I can think of to help is to move them to a safer location.
A third danger is wind. A lot of people will lose power because of wind. Trees will come down and block roads and cause property damage. Especially with that cold front meeting Sandy, I don’t know how strong the winds might be for you. You probably can’t do a whole lot about trees blowing down or limbs falling off. Try to pick up or secure debris that might become a missile. These things spin counterclockwise. Use that to determine what direction the wind will come from. In Virginia with the current forecast, North is certainly a concern. How much East or West winds you see depends a lot on where you are. It looks like a South wind won’t bother you at all. That may make your preparations a lot easier.
If your coop is well anchored, your chickens in it should be OK. In these events you are mainly looking at survival, not comfort. It won’t hurt them to be wet for a while if rain does blow in. It really won’t hurt them long term if they go without food or water for a day. They will survive and recover.
Yours in the runs are a lot more of a potential problem. I don’t know how strong those are built or how exposed to the wind they are. They need some kind of protection from a north wind and possibly a bit from the east and west. I would not worry about protecting the entire east and west; just try to form a pocket to the north with some side protection. The rain is probably not going to be coming straight down either, but something over them to help keep them dry would help. I don’t know how to tell you to do that with your situation. That depends on how your runs are built and what materials are available. Tarps might work if you can really secure them. Maybe plywood? Whatever you put up will present a solid wall and pick up a lot of wind force. If you put something flat on top, that can see a lot of uplift.
I really don’t know how big a danger storm surge or rainfall is to you. That really depends on your local conditions. The ones in your coop should be OK from wind. From what I understand of your situation, my emphasis would be on figuring out some way to give the ducks and chickens in your runs a protected pocket to the north. With the projected track I’d usually think most places in Virginia are not in that big a risk, though these things can be pretty unpredictable. But with that strong cold front merging with it, I don’t know how bad it might be.
I know this is long and drawn out but I’ve tried to show my reasoning. You don’t need to waste effort and thinking by panicking over things that are not a real risk for you in your location. You need to take reasonable precautions. I really hope Sandy becomes a non-event for you and a whole lot of other people, but I am really worried about people further to your north.