How big are the holes? If they are small fill them with caulk. If they are large holes,the best thing to do is replace the siding in the area of the holes. thats if you have leftover siding around. If you don't and can find siding the same color at a store, remove a piece of siding from a inconspicuous area and put the new in it's place and use the removed piece to replace the areas with the holes. You can find instructions online. look for repairing vinyl siding. They also did this on this old house last year.