Balance of power?

OK...I know I'm a product of Schoolhouse Rock and all the idealism that it presented. But something about the funding of the court system, from top to bottom, just doesn't sit well with me. The court is not employed by the commissioners, judicial is not an employee of legislative, but yet the budget is news in more than one county. Costs and availability of funds seem to drive the decision-making process much more than the suitability of options for juveniles in need. I've even seen it at work in my own county, at the common pleas level, so I'm sure it runs the entire spectrum of the court system. It just leaves me wondering who really is in control and how are they making the decisions?