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When you estimate an expense in Projects so that you can track that expense against what you budgeted for it, and tell Projects that you'll be on-charging at a particular rate, Projects tracks the progress of expenses incurred against the revenue expected. It should be tracking the progress of actual expenses against the estimated cost of that expense.

In the screenshot I've attached, you can see that the expected total cost of the expense I'm tracking is $202,702.50 and I have so far used $140,257.52 of that. It should show that there is $62,444.98 remaining in the budget for this particular expense (before it starts cutting into the profit margin). Instead, it's tracking the costs against the expected revenue of $249,480 and is counting down the value remaining before I make zero profit on this expense and have nothing left to cover overheads.