How do i use passports for US and Japan?

I'm a dual citizen for Japan and US, and I currently live in US. I wanted to experience living and working in Japan for about 2 years. I'm currently 22, but I made sure to make a Japanese passport before I turned 21. But I was wondering how do I use it? I know you use the US passport in US, and Japanese passport in Japan. But when I decide I want to go back to US, wouldn't Japan wonder, how long I'm gonna stay in US? cause technically, they don't know I'm US, but wouldn't I have to show both passports to prove that I can stay longer than 90 days in US, and I don't need a esta too?

You'd leave the US on your US passport, enter Japan on your Japanese passport, leave Japan on your Japanese passport, and enter the US with your US passport again. The two countries wont care what other stamps may or may not be in your passports since you're a citizen, so it doesn't matter.

The only thing to be careful of is the name you use on your plane tickets need to match the passport you're using for identification. So if you have two different names on the passports you need to make sure the plane tickets have the name of the passport you're LEAVING on. IE, when you head to Japan, make sure the plane tickets are in your US name, and when you leave Japan in the future, it should then match your Japanese name. Obviously if the names are the same on both passports, it doesn't matter and you can disregard that.

Firstly, there is no passport control when leaving the US, so it does not make sense to say "use your US passport to leave the US".

Secondly, check-in for your flight and exit passport control (in Japan) are different things and you are not required to use the same passport for both.