When I approach a charter school budget, especially for a school that has very tight finances or is financial trouble, I look at the payroll line. More specifically, I look at the detail of who is on payroll, salary by position, and total payroll as a percentage of revenue.
Because I work with multiple schools, it's easy to compare against other schools. The difficult part is that due to the differences in methods between charter schools, it's often hard to distinguish which employees need to be on staff and which don't.
I often begin with the administrative staff because administrative areas are the ones that schools have in common. If two schools are roughly the same size, then they should have similar administrative staff budgets, but often they don't. This can be caused by some schools doing more than they need to do. Some schools, often due to very controlling directors or principals, end up tracking even more than is important for operation and compliance. It also can be due to directors simply not really knowing much about administrative functions. That's a reason that some schools outsource administration or finance. This can also happen when schools hire their own custodial crews. They often pay much more than they need to.
The academic staff is a much more touchy subject. Often schools have built an untenable staffing model. Because of their desire to serve children and their educational methodology, they think that they have to employ a certain number and type of employee. The over staffing can be due to excessive numbers of tutors, extremely small class sizes, a variety of specials and extra-curricular activities. It can also be due to a desire to provide additional counseling assistance. None of these desires are bad. In fact, they are the opposite. However, when the budget cannon handle the number of staff, then something has to change. Because charter school leaders (and often board members) are idealists, they don't want to cut staff or change their model. They fall in love with their model. The problem is that the financial model doesn't pair with the academic model, and the financial model isn't going to change without substantial external funding.
Too many charter schools try to make this up through grants. The problem is that their isn't enough grant money available to cover all of the charter schools who want to employ additional teachers and tutors to implement their academic model.
While it isn't the only place to cut or rearrange, payroll is always the largest expense for a school. There just isn't usually enough play in the remainder of a budget to create additional positions. A payroll and benefits budget can be 70% of a charter school's budget. Because facilities is usually between 15% and 20% of a budget, there simply isn't much room to cut the other expenses, especially when most of those are not really discretionary.