We have a custom .NET web application that will be connecting to SharePoint over SharePoint's API primarily to store documents in SharePoint and take advantage of the document management functionality like check-in/check-out, versioning, etc.
We will not be using the SharePoint UI at all. The custom .NET web application is the only UI the user will see (SharePoint in the background for document storage).
Question(s): Is there a way to search across all Site Collections and their subsites? What is the process?