Just to start from the top
You don't need all projects in a single solution but it does make it easier, so I will assume you will at this stage.
Add in your second project to your solution.
On your Azure project (MySite.Azure), on the Roles folder, Right Click and press Add > Web Role Project In Solution and add in the other project to your Azure project.
Next in your ServiceDefinition.csdef in the section
<Site>
<Site name="Site1" physicalDirectory="C:\Users\User\Documents\Visual Studio 2012\Projects\Project1">
<Bindings>
<Binding name="Endpoint1" endpointName="Endpoint1" hostHeader="domain1.com" />
<Binding name="Endpoint2" endpointName="Endpoint2" hostHeader="domain1.com" />
</Bindings>
</Site>
<Site name="Site2" physicalDirectory="C:\Users\User\Documents\Visual Studio 2012\Projects\Project2">
<Bindings>
<Binding name="Endpoint1" endpointName="Endpoint1" hostHeader="domain2.com" />
<Binding name="Endpoint2" endpointName="Endpoint2" hostHeader="domain2.com" />
</Bindings>
</Site>
</Sites>
<Endpoints>
<InputEndpoint name="Endpoint1" protocol="http" port="80" />
<InputEndpoint name="Endpoint2" protocol="https" port="443" certificate="SSLName" />
</Endpoints>
This shows 2 endpoints as well for SSL usage.