What happens if clouds go in front of the sun while I'm cooking?Edit
Your food will continue to cook as long as you have 20 minutes of sun an hour (using a box cooker). It is not recommended that you cook meats unattended when there is a possibility of substantial cloudiness. More information on this see Food safety. If you can be sure that the sky will stay clear though, you can put in any type of food in the morning, face the oven to the south, and the food will be cooked when you get home at the end of the day.
If serious cloud cover significantly more than 25-30 % moves in and looks like it's there to stay, you need to save the food by moving it to some other kind of cooker. If your food is basically done (or near to and still very hot), and you're just keeping it warm enough to be safe and tasty until mealtime, you can tuck it into a box (or leave it in the box cooker, if that's what you're using) with insulation such as old quilts or comforters or sleeping bags tucked around it before closing the box and it will stay hot for at least a few hours. If the food definitely needs more cooking or has cooled into the danger zone, what will best emulate the gentlle heat of your solar cooker is an oven turned low (between 200 and 250F, depending on how much cooking the food still needs and how much time you have to reach it in). Electric slow cookers (aka crockpots) can also provide a good save for underdone foods such as soups, stews, etc. You can also use a stove burner, but if you want to retain some of that special flavor of solar cooked foods, keep the heat on the low side or use a diffuser on the burner. None of those options use as much power or heat up your kitchen as much as burners on high or higher oven termperatures.
Solar cooking frequently-asked questions - Solar Cooking
http://solarcooking.wikia.com/wiki/Solar_cooking_frequently-asked_questions