Basically, the supplementary appropriation bills and the estimates are to top up the annual appropriation. They are ongoing expenditures of departments—running expenses of departments, if you like.
At the same time that the supplementary estimates are presented, the departments present their estimates of expenditure under their special appropriations. For example, the whole social welfare program, as it used to be called, is contained in special appropriations. It's not in the annual appropriations; it's contained in the other statutes.
All the expenditures are elaborated in the estimates and are open for examination at the time of the estimates hearings.