I think a useful place to start is building up general programming chops and learning godot (if that is what you want to make it in). There are many ways of building something like this and after you've reached a certain maturity with coding you'll know how to make it in a way that fits your goals.
That said I'll briefly describe how my program works:
1. I have a dictionary that maps coordinates on the tile grid to objects
2. Objects can be blocks, enemies, items, etc.
3. Through the UI, the player may add/remove objects to certain coordinates by interacting with cells in the tile grid
That's the short version. Obviously there is a lot of implementation details in each step. Maybe one day I'll find time to write a more in-depth explanation on the games website.
