If you don't want to upload and replace complete application with your existing application then you need to do the following steps.

1- Before update must backup your database and application folders and files.

2- You do not have to replace all the application folders every time. 

Just the following specific folders are important to replace and your application will be updated to latest version.

Folders include are: 

• app
• resources
• config
• database
• routes
• vendor
• js
• css
• node_modules
• Files include
  • composer.json

3- Open your website or application in a browser, login as admin then go to settings -> general settings -> Important update option and click import. This will update your database.

Note: You must backup your application and database before applying update. After updating the application  you can replace your custom.css file from your backup.