Hi,
There are 2 ways to push your project to the cloud. Publish or Package.
Publish usually takes time due to various factors like network latency and traffic.
the other option to Upload the Package (.cscfg and .cspkg) are uploaded directly from the Management portal and is much faster. The package approach is best practice as the deployment method since you can maintain a backup too.
refer to the following link:
https://azure.microsoft.com/en-in/documentation/articles/cloud-services-how-to-manage/
You site will not be down as long as the SLA requirement of atleast 2 instances are met.
Regards,
Nithin Rathnakar