I always irrigate any open wounds prior to prepping. In this case, you would use CHG or betadine. Start by packing the open wound with sterile gauze first, and then using another sterile sponge, prep around the periphery of the wound outward. When you have prepped from the edges of the wound out toward the periphery of your surgical site, then remove the gauze and with another sterile prep sponge, prep the wound.
If you were prepping an area where a stoma is present, you would clean the stoma and then cover it with an occlusive dressing such as Tegaderm. Then you would prep from the edges of the stoma outward.
Did that make sense?