If you provision an all-inclusive SQL Server virtual machine from the Azure Marketplace then you’ll be charged a single fee which includes the cost of SQL Server. If you want to bring your own SQL Server licences to that virtual machine via the Azure Hybrid Benefit, then you need to change the licence type of the virtual machine. You do this in the Azure Management Portal and simply change the licence type from Pay As You Go to the Azure Hybrid Benefit in the Configure settings of the VM. You can find instructions for that here: http://bit.ly/2Pd6miy.
If you’ve self-installed SQL Server on an Azure virtual machine, then again, you’re probably intending to bring your own licences. The Product Terms states that you need to indicate when you’re using the Azure Hybrid Benefit – which is what happened above – but this time you need to first register the SQL Server VM with the Resource Provider, and then activate the Azure Hybrid Benefit as before. You’ll find instructions for the process of registering a SQL Sever VM in Azure with the SQL Server VM Resource Provider here: http://bit.ly/324kGLx.