I have created an Azure Web Site and connected it to Visual Studio Online, and this automatically set up a continuous deployment build (as per this page).
Initially
You can override the deployment engine in Kudu by using the Azure CLI Tools. Running the azure site deploymentscript command and passing in the parameters for one of your projects -s .
This will create a .deployment file and a deploy.cmd (or deploy.sh if you pass the -t bash parameter) modifying the deploy.cmd to add build/deploy steps for the second project.
More information is on deployment hooks is available in the project kudu wiki.
EDIT
You can use App Setting COMMAND to add a deployment script to your site.