You've stumbled over one reason why I frequently say Project is not a
replacement for accounting software. It's the accounting system that should
be tracking the overall finances of the firm. Project's budget is only a
small part of that, one contributing expense out of many. If I have a
resource that gets $100 per day and I use him for 4 hours on one of the days
in my Project, the cost to the firm may well be $100 but the specific cost
of using him in my project for that day is $50. The other $50 is part of
the firm's overhead (if he didn't do anything else) or part of the budget
for whatever it was he did the other 4 hours of the day but emphatically
should NOT be included as part of the project's costs. MS Project does a
good job of tracking the actual budget of the project but it's not intended
to track the impact of those costs on the overall budget of the firm. Look
at it this way - the project budget, which consists mainly of resource
costs, is the cost of doing that specific project. If we didn't do it at
all, the budget *for that project* would be zero even though the firm would
still have to pay out the same amount of money in salary to the resources on
staff.