It would be ideal to follow the same structure you are designing for each kind of module ("folder").

It will make the code more maintainable.

Just keep in mind that nothing is set on stone, you can adapt from project to project and check other software engineers ideas as well...

If you would try the same but with NestJS then you would already have a better guidance on how to follow it. If you would like to take a look on NestJS framework over Express, try this friendly link: https://makinhs.medium.com/graphql-nodejs-postgres-made-easy-with-nestjs-and-typeorm-4daff3c516d?sk=813224fbe4231534871c185e4792e3e3