Hi Julien,
I think you might want to look at a document for our web services, called "Web Services Primer".
It has a clear example of PowerShell commands that can allow you to wrap flows and trigger them remotely (Or from another application that would run the commands).
I think it may be useful for what you are considering as well.
Note: The 1.1 revision of that document will be out soon, with the official 1.1 release.
Yaron Haimsohn
WFA team