Yes, you can do all of this in code. The Tiled world is much different than the rogue world. I am familiar with rogue and angband and nethack and all of the flavors in between (Moria!), and even tried to make a nethack for Qualcomm Brew long long ago.
In tiled you will need to make layers, and in those tiled layers, you will place your world tiles, objects, etc.
When cocos2d (all flavors) reads the tmx file, it programmatically makes the tile maps just the same way that you would. There will be a lot of plumbing on your part to do the sprite sheet links for the tiled tiles.
Great project! We are here to help if you need it. We are the maintainers of the cocos2d-xna side.