@Praful Lele Thank you for your question.
Yes, we do support the deploying of multiple .war files. I currently have steps on how to do this via CLI, PowerShell, Kudu API, and Kudu UI.
Please see here for steps on how to create a zip file of your .war files and then deploy them. The special callout since you are deploying multiple .war files is to for apps different than root, use:
/api/wardeploy?name=myapp
You mentioned specifically via ARM template. Can you please share the ARM template you are using if this is your preferred method so I can look at it further and advise you if any changes are needed?
I hope this helps get you going and look forward to your reply if you require assistance with the ARM template.