Livery colours were neither fixed, nor subject to the rules of heraldry. The tradition of wearing blazer badges on the left breast (close to the heart), stems from liveries... but larger central badges were common too.
"Sable over gules" would refer to the livery standard. All the images I've seen reconstructing Buckingham's livery jackets have red on the wearer's left and black on his right, as did the badge used without permission by Buckingham Town Council in 1566. More recent badges derived from the livery (Buckinghamshire, Aylesbury F.C. etc) routinely reverse the colours each time they are re-imagined for a new use.
The white swan, the knot and waterwheel are all badges associated with the family. There is a train of thought that each badge was attached to a specific title held within the family, but were hereditary. So for argument's sake, the 'Duke' had the Swan, his eldest as Lord Stafford had the Knot and perhaps the second son as Lord Somewhere Else had the wheel. Only if an individual possessed all of the family titles did they all appear on his household standard. It would certainly explain why some nobles bore a single badge, while others had two, or in the case of one of the Percy's four.
This could extend to the men raised from the lands associated with the titles, so men from the duchy marched under the Swan, men from the Manor of Stafford under the Knot and so on.
Nothing to prove this of course, but it does make a certain sense of why some badges were used and others were not at various times.