I sketch out the maps on paper or digitally before making the actual pixel art. It usually helps with coming up with puzzles too if it's that sort of game.  Usually I make a separate file with a collage of references and on obsidian I write up the cutscenes and story stuff in parallel so I won't leave spaces where nothing happens.

Hey thanks for the advice! I'm having issues with the geography of mine, but this helps a lot

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