If the Virtual Machine is stopped from inside the VM by issuing a shutdown command, It will result in a Stopped (Allocated State). In this state the VM is charged for the CPU and memory allocation and not for license. When a VM is shutdown from the Azure portal it gets to a Stopped (Deallocated) state, where the VM is not charged for any resources. Note: the VM image stored in the storage still will be billed for the normal storage rate.
Shutting down a VM when not in use, is a great cost saver. One can choose to shutdown or boot up a VM any number of times depending on their business needs. Here is a quick reference for automating this if you need.