There is no transit from International to Domestic. This is fairly standard in most countries as you need to formally pass through customs formalities with your bags. On the way out (i.e. leaving the country) though you can check straight through as there is no outbound customs check.
You could take Peach, but be aware they operate from a different terminal at NRT. JAL is Terminal 2, Peach is Terminal 1, so you will need to allow time to get between terminals. For ease of transfer, JAL or Jetstar Japan will be easier. Jetstar Japan leave from Terminal 3 (the LCC terminal), which is a 10 minute walk away, but they have a check-in counter in the arrival area of Terminal 2.
If you use JAL and use the Japan Explorer Pass or Yokoso Pass, the ticket will be issued in conjunction with your international ticket, so that will give you some protection in case of a delay. Not so if you have Peach or Jetstar though. The cheap fares are use it or lose it.