You should deploy the hotfix according to hotfix instructions for remote installation.
You can find hotfix instructions in the folder you’ve installed the hotfix package to (probably
Basically you need to deploy the hotfix files using the deploy parameter locally, than copy them using FTP to your web site and apply hotfix sql script to you database and you should be done.
We recommend you to backup both you Azure web site files and the database before the process.
Best Regards, Zbysek