This is an example of how I'd set up a basic Express + SQLite app.
The SQLite connection is defined in src/database/db.js. This will read the DB_FILE environment variable and connect to the corresponding DB (or create a new one if it doesn't exist). It will also run the statements in src/database/schema.sql to ensure the DB contains the right tables.
This DB setup happens whenever the server starts, so make sure the schema.sql commands are safe to be re-run.
You can seed the DB with some example values by running npm run seed. This will execute the commands in src/database/seed.sql, which will insert some data.
The local dev npm script sets DB_FILE to db.sqlite, which is listed in the .gitignore so each local user can have their own copy of the DB.
Make sure you set the DB_FILE env var in your production environment. This might need to be in a specific directory (e.g. on Glitch only the .data/ directory is persisted).
Important
Most "Platform-as-a-service" hosts like Heroku are "ephemeral"—they recreate your app every time you deploy (and sometimes more often). This means the filesystem does not persist and your data will be lost.
SQLite should be used with platforms that either allow attaching a persistent volume (like fly.io), or just give you full control over the computer you're deploying to.