Thanks a 1 + year after you answered ! Sorry about that.
Well we have decided to track only PTO in the timesheet for those entering time. If a resource is not entering time, then they or their manager can enter time off into a PTO project. I know that this is not the best but only about 50% of our teams will be using Project Online TT to save $$.
We will have a Admin/People Management project and Training project. This will let managers to assign time for their team members. Everyone can then see ADMIN and Training time demand on resources in the Resource Center.