I would say your Golden Comet laid the darker one and the Rock, the paler one. Welsummers lay dark brown/terracotta coloured eggs, often with speckles. It is odd that you are getting two dark brown eggs. Are you sure about your other breeds? You haven't got a Black Copper Marans instead of an Australorp have you?
In my experience, Sussex lay torpedo shaped eggs which are pale pinkish cream coloured with a nice sheen to them. 
I would say that last one had a good chance of being a Golden Comet egg. Those hybrids seem to be more likely to lay a matt finish to their shell with additional chalky calcium deposits making those white spots.
These are mostly generalisations though and variations occur within any breed.
To use food colouring, use a paintbrush to dab a little of the liquid on the lower lip of their vent right at the opening whilst they are roosting at night. When the egg is laid the next day, the wet bloom on egg will cause the food colouring to stain the egg as it is laid. Do not use red food colouring on any of the hens as red can encourage other hens to peck the vent and cause injury. Do one chicken a night if you only have one colour or use different colours for different chickens and keep a record.