There is a web.config key available in Kentico which serves the very purpose you are looking for. The key I am writing about is CMSAzureRootContainer - its description is following:
Specifies the name of the blob container that will serve as the root of the application's file system on the Azure storage account.This can be useful in scenarios where multiple applications use the same storage account.The default value is cmsstorage.
The value parameter for the key represents the container which will be used, for example:
<add key="CMSAzureRootContainer" value="CustomRoot"/>