Nonprofit accounting is fund accounting. Instead of tracking one pool of money toward a profit figure, you track money according to the restrictions donors attached to it, and you report spending by function as well as by type. Ratios sit on top of that structure. They only mean something once the structure underneath them is right.
Most small organizations get the ratios wrong because they got the bookkeeping wrong first. A program expense ratio calculated from a chart of accounts that never separated program from administration is a number with no content. Start with the structure.