2D JRPG Structure and Design

I want to do my own take on a 2D JRPG style of game. (Something like this: http://www.vizzed.com/videogames/snes/screenshot/Final%20Fantasy%20III-3.png)

I’m planning to use Paper2D, but I’m not really sure how to set up the scene for everything. I’m only familiar with doing a 2D side scroller platformer type game, where the camera moves and you go around the level. I’m not sure how to begin doing a 2D game where everything stays still.

This question just pertains to battle scenes. I don’t plan to have an overworld, just a main menu and battle scenes.

But, I just can’t figure out where to start with this. Is there a game mode or template which would fit this style? How would I handle the transitions between the menu and the battle scenes? Just change the levels?

I’m completely lost on how to get started with this, as well as the structure needed. I feel that once I knew of a good place to start, things would fall into place a letter better in my head.