It is best practice to separate each application that will be automated into its own project and then use a controller project to orchestrate and control the workflows/use cases.  For example, if I need to automation application abc.com, xyz.com and application bcd I'd create four separate projects; one for a controller project (e.g. MyDesktopAssistant) and three projects, one for each application.  Each project can then be treated as a standalone development solution for each developer.  They would develop and test all of the automations needed for their assigned application.  The external API to the project would be defined through Activities.  For example, if you need to retreive address data from application abc.com you would create an activity, GetAddress, that the controller project could start and the abc.com project would pick up via an ActivityStarted event for that activity, the abc.com project would execute the necessary automations to obtain the address and return the information either via the activity parameters or if an interaction context is being used via context varialbles.

Then to pull the entire solution together you would simply use the add exiting project to reference the application projects from the controller projects.