When changing substrates its beat to remove the fish and plants into buckets while you change about the substrate in the tank. Once you switch the substarte its probably wise to do a rather large water change (maybe 70%) becuase chances are the water will become really cloudy and/or polluted from disturbing the substrate.
The change of color substrates wont matter to fish or plants really. Unless you are going from nutrient packed substrate to an inert one. Plants can possibly melt a little from just not liking being transffered/moving around. Lighter colored Fish can potentially darken to match the substrate color vetter, some fish are said to show better colors against darker substartes, but I think its just contrasting colors tha make it pop and not the actual fish brightening up, although fish could possibly brighten up if feeling happier/safer with the darker substrate.
Biological bacteria should manly be in the dilter mesia because of the better flow. Some will be on the tank walls, decor and substrate, but are minimal, so you shouldn't need to worry about keeping the beneficial bacteria from the old substrate. The new substrate will colonize shortly.