I agree with other posters on many points.
As an ordinary Japanese, I will talk about a typical Japanese home traditional breakfast.
In Japanese language, we usually call meals ggohanh, or in a casual way gmeshih. These two words mean fundamentally gcooked riceh, because since old time, having meals has been nothing but eating rice. Other stuffs like miso soup, cooked or raw egg, natto, pickles, nori, fish (in ordinary ryokan, often served a piece of grilled salmon, of low quality!), etc. are served to make rice more nourishing.
If you observe Japanese ordinary people eating their ggohanh, you easily notice that they often have a bowl of rice in one hand, and using ghashih (chopsticks) with the other hand to pick up other food, and they put down the bowl of rice on the table to take a bowl of miso soup instead, or put the two bowls down on the table to eat other food with more gconcentrationh.
In ryokan (except low ranked ones), they often serve too plenty breakfast, but in my personal opinion, this is not a traditional Japanese breakfast, because in Japan, traditionally, a breakfast is simple and frugal. But, nowadays, in ryokan, a gkaisekih style of breakfast is served; this is not a typical traditional Japanese breakfast, either. If all food is already prepared on the table, you remember what I have explained.
As for natto, this famous food of disgust for foreigners (especially westerners), you donft eat it as it is, without seasoning. A usual way of eating natto is to add a reasonable quantity of soy sauce (to make it enough salty), a little bit of mustard and fine cut gnegih (sort of leek) and to stir it swiftly and fully (more than fifty times if you like, until the whole becomes gooey and slightly whitish, and then to pour a proper amount of it on the rice and spoon up with chopsticks a mouthful of rice and natto. In this way, you can have less smell and more taste (umami).
Anyway, in no matter what order you eat the food, you never offend Japanese people.