Youtrack Upsource integration and shared project requirement ?

Hi.
I'm working on integrating our existing youtrack system with upsource to get vcs info in youtrack cases etc.
The youtrack database has been used for years with many cases and projects, the upsource install is new.

I fail when trying to set up the integration and I get the impression that youtrack and upsource must be configured with the same/equal projects?
If so I find that somewhat strange or that we have configured youtrack in a bad way...

Our youtrack/case setup is very customer, and product, focused. We have multiple projects for managing multiple customers/products etc.
When setting up upsource I want to have this more focused on the vcs structure which is cross customer and products.
Our upsource setup could have far less projects than youtrack.

Have I misunderstood how youtrack+upsource should be integrated/configured?
Is it possible to get this integration with 'cross-projects' in the hub?