I was just searching this same topic hoping that there had been some updates made.

I too get bills from one subcontractor which has specific amounts that need to be applied to 8 separate customer projects. It would be nice to see an update that doesn't list the whole bill but here is what I've found.

If you go to a project and then to the transactions tab, it does list the full amount of the bill, which can be confusing however under the costs section of the project, it only lists the specific amounts to this project.  The project profit margin does not calculate based on the full amount of that bill, just the amount specifically tagged to that project.  

I hope this helps :)