Any delicate area is difficult to keep clean, especially when trying to alleviate using a disinfectant with harmful chemicals and ammonia. There are some simple ways to keep a whelping area clean without any harm to the "residents" using the area.
Chlorine bleach is a trusted choice for cleanliness with no harmful side effects. You can make a solution of bleach diluted in water in a spray bottle for easy cleaning. Be sure the area is completely dry before pets use it. Bleach disinfectant wipes can work as well.
If you are eco-conscientious, a number of commercially available natural cleaning products are safe for the whole family and your pets. They offer a broad spectrum of antimicrobial disinfectants and deodorisers and generally considered safe to clean pet kennels, toys and the whelping area.
Tea tree oil is a natural disinfectant when mixed with water and adds a pleasant scent to the whelping area. Borax is a naturally occurring mineral, antifungal and disinfectant when dissolved in hot water. A spray of diluted hydrogen peroxide acts as good disinfectant. Vinegar is most effective as a disinfectant when undiluted. It removes mildew and is not likely to pose any environmental or health hazards. Baking soda works well as a natural cleaner and disinfectant as well for safe cleaning of the whelping area.