Currently I’m working on a 3D video game, the modelling for which I just use Blender. My world isn’t big enough to warrant thinking about it on paper nor especially anything digital. Currently it fits in my head just fine.
2D video games vary more technically and stylistically, so it’s hard to say which tools I’d use. My previous game, Barry Red (which I never finished because of broken game logic) had one large background loaded in chunks, also made with Blender. If the game were tile-like I’d make levels with Tiled, instead. Maybe you’ll want something in-between, like loading premade sprites in the right places, them together forming a single shape.