I try to create only Project Milestones, but I have a situation where I have to use Global Milestones.
We have a Project that tracks new feature development in a product, and Projects that track Customer Support issues in the same product. Various FogBugz features that we use make it necessary that these are separate Projects, however the product release date corresponds to a Milestone that has to exist in all affected Projects. I use Global Milestones to do that. The Global Milestone reports show information on all developers and projects that are affected by those global milestones (as long as the Cases are above the Priority threshold for the report, they are assigned to developers and they have estimates). Project Milestone reports are the same, but for individual projects.
If you have developers multitasking, you can get them to identify the % they are working on each Project using My Settings -> Working Schedule -> % time spent on FogBugz tasks:. I assume this is used by EBS, but we have only just started using that feature so I'll leave it up to someone else to comment further.