@Jan Vávra - Ideally if you have a server with SQL and other application installed on your server. Then system state backup will install the system files in it and ideally you should install the application separately to bring it up.
Also, in this situation BMR backup is better option as it gets the application also restored if it is installed on C drive, but MARS does not support BMR backup. You should use WSB or DPM\MABS to do BMR backup. But as you have mentioned that it is a Azure VM so BMR restore is also not supported on Azure VM.
The best solution for you would be taking Azure VM backup from Azure portal which could help you to restore the VM in case of disaster.