What is the best way to use socket.io with expressjs app?

You can use http with express app and then connect sockets through that http connection and you can listen and emit the topics inside the io.on('connection')

const app = require("./app");
const mongoose = require("mongoose");
const http = require('http').Server(app);
const io = require('socket.io')(http);
mongoose
  .connect(`mongodb://localhost:27017/${process.env.DATABASE}`)
  .then(() => {
    app.listen(process.env.PORT);
    io.on('connection', socket => {
      console.log('socket connected',socket);
    });
  })
  .catch((err) => {
    console.error(`connection failed: ${err}`);
  });

I will prefer this second way:

App.js

const express = require("express");
const pug = require("pug");
const app = express();
module.exports = app;

Server.js

const app = require("./app");
const realtime = require("./realtime");
const mongoose = require("mongoose");
const server = require("http").Server(app);

mongoose
  .connect(`mongodb://localhost:27017/${process.env.DATABASE}`)
  .then(() => {
    app.listen(process.env.PORT);
    require("./realtime.js")(server);

  })
  .catch((err) => {
    console.error(`connection failed: ${err}`);
  });

Realtime.js

module.exports = (app) => {
    const io = require("socket.io")(app);
    io.on("connection", (socket) => {
      console.log("Socket connected")
    })
};