This might sound like a no-brainer, but one important rule for storing your bulk food items is to keep them away from non-food items. You don't want to keep the sugar next to the rat poison and dishwashing detergent or boxes of cereal in the same cabinet as your window cleaner. Storing food near potentially dangerous materials like this increases the risk of cross-contamination.
You'll also want to keep any bulk food in the refrigerator away from raw meat, fish, and poultry to prevent cross-contamination from these foods, which are prone to carrying bacteria.
On the flip side, it's a good idea to keep your bulk foods away from easily damaged paper products. Store paper towels, napkins, and paper dishware on a higher shelf, if you do have to store them in the same cabinet as your bulk foods. One busted jar of tomato sauce can ruin months' worth of paper goods and negate a lot of the cash you saved by opting for bulk food in the first place.
Toxic chemicals and bacteria can contaminate your food, but you also want to make sure you store bulk items away from heat and water sources, because these can shorten their shelf life.