There is a LOT more to the environment of the digestive system when it comes to beneficials and parasites.
What about the pH of the colon for example? when the correct fermentation of carbs and different fibres takes place, there will be an increase of short-chained fatty acids. These in turn feed cells of the bowel, improve its health and help beneficials to grow. Ensuring carbs are properly broken down and fully fermented is one of the chief aims of my dietary approach. And eating the right fiber is in fact one of the most important factors here. The gums and pectins found naturally in vegetables and some fruits are more favorable than wheat and oat bran. The better the bacterial fermentation of carbs (and the more the improved digestion in general) the better the beneficials.
When it comes to parasites, I tend to think of SIBO, or Small Intestinal Bowel Overgrowth, which may include parasites, yeasts and various protozoan and bacteria.
SIBO occurs more easily in a person who has an underactive stomach or pancreas. Enzymes help here tremendously.
Use diet predominantly, but most folks need probiotics, enzymes and different kinds of antifungals. Fatty acids are mostly forgotten. I really don't believe that it matters when you take the supplements, as long as you take them.