The best time to take probiotics is first thing in the morning, on an empty stomach. Remember that probiotics are a live bacteria. Look for a product that has been kept in the refrigerator. A product stored at room temperature will have a significantly reduced potency.
Supplementing with digestive enzymes will go a long way with helping your body digest and utilize the food you eat. As bodybuilders, we are constantly overloading our digestive systems with the amount of food we eat. You don't need to take them with every meal but I would supplement 2-3 meals per day with digestive enzymes. Look for the ingredients bromelain and pepsin as these enzymes help digest protein.
GEAR by n2bm.com is a fantastic supplement. It contains super plasma serum, BCAA and digestive enzymes to help with absorption.