It's a government decision to allocate spending in the supplementary estimates or to seek spending in the supplementary estimates. The decision to allocate spending is usually made in the budget by the Minister of Finance and the Prime Minister. Depending on the state of advancements of each proposal, they're either tabled or included in supplementary estimates (A) or (B), and whether they're in supplementary estimates (A) or (B) determines how advanced they are in their development and whether there are enough details for central agencies, notably the Treasury Board Secretariat, to determine whether they can let that go in supplementary estimates (A) or (B).
The categories under which they fall are by their own definition and the very nature of these expenditures. If the Department of Indigenous Services, for example, is seeking money to deliver on programs, it is operational money. On the other hand, if it needs capital spending to build infrastructure, then it goes into capital expenditures, which is a different vote structure under the Treasury Board methodology or terminology.