I need help how to think about designing our application to fit into the new Azure Service Fabric template.
Today we have an application built on Azure Cloud Service
I think you have the right idea, in general terms, that each bounded context is a (micro) service. Service Fabric gives you two levels of organization with applications and services, where an application is a logical grouping of services. Here's what that means for you:
Logically speaking, think of an application as a cohesive set of functionality. The services that collectively form that cohesive set of functionality should be grouped as an application. You can ask yourself, for each service: "does it make sense to deploy this service by itself without these other services?" If the answer is no, then they should probably be grouped in the same application.
Developmentally speaking, the Visual Studio tooling is geared a bit more toward multiple services in one application, but you can have multiple applications in one solution too.
Operationally speaking, an application represents a process boundary, upgrade group, and versioning group:
Placement and scale is done at the service. So for example, you can scale one service in an application, and you can place another service on a larger VM.