Gaijin doubts – Hlhow to eat in a Japanese restaurant?

I'll be spending 16 days in Japan in August between Kyoto and Tokyo and, being a foodie, I intend to visit as many izakaya as possible.

I have seen photos and videos of Japanese meals and I noticed that they are composed with a bowl of rice, a bowl of protein, some miso soup and some side vegetables.

My questions are very straightforward: how do I eat that?

1. Should I start or finish with the miso soup?

2. Should I add the protein on top of the rice and eat it as a lump or eat it separately (like: one piece and protein and then a bit of rice)?

3. Am I supposed to hold the rice bowl and shove it into my mouth? My chopsticks skills aren't good enough to hold it from the table to my mouth!

4. What dishes do you recommend? I prefer fish.

Thank you