As your service is based on CloudLinux you have control over php.ini setting per each of your domains.

To increase maximum upload limit in php.ini please follow these steps:

1. Login to the cPanel of your domain. (This is the cPanel of that domain not the main WHM account)
2. Click on "Select PHP Version"
3. Change to PHP version to anything that is not native and click on "Set as Current"
4. Now from the top right side click on "Switch to PHP Setting"
5. Now from the list click on the value next to upload_max_filesize and change it.
6. Click on Apply
7. Click on Save