Fat soluble vitamins and supplements should ideally be taken with a fatty meal for best absorption. Multivitamins are best absorbed on an empty stomach but often they can cause an upset stomach. If so, then it's ok to take them with food. I would take the enzymes before a meal so they can do their job (break down proteins) and the probiotic should probably be taken on an empty stomach or with a light meal so that they can stick to your gut.
Like daz said, follow the instructions on the bottle.