I would mention three things. I think there need to be well-placed coordinators in the different agencies to do this. There needs to be someone whose role it is, at least in part, so that when people in the agency or department have questions, they know who to go to. It helps if it's somebody within their organization rather than somebody out of central office.
Second, I think there needs to be coordination across the ministries. While you want to let different types of analysis happen in different types of places, it still has to be coordinated. It has to all feed into the same set of numbers. If you have one agency doing something very different from what's being done in another agency, that can be a problem. If the goal ultimately is to have a comprehensive budgetary plan—which is to me what a budget is, a comprehensive plan for spending and revenue raising—then there needs to be coordination among the agencies on how to do it.
Then, third of all, I can't emphasize enough that training is important. I've seen it with a lot of things beyond budgeting. If people don't know how to fill out the forms, they may well put down some numbers and do some reports, but who knows exactly how useful that will be? I think there needs to be a kind of education—professional development, really—so that the people who are doing the work know how to do it and talk to each other, and there's a trading of ideas and a kind of constant professional improvement and development.