I am certainly not a CPA but here are a few nonprofit bookkeeping tips and advice I have learned along the way.
1. I am very glad that I can enter my programmatic budgets into Quickbooks. First, I associate each program with a class in QB. For example, Aspiration's Field Community Building program is a class. Second, I associate each project within each program as a subclass. For example within the Field Community Building program there is the Penguin Day class.
2. I also designate in QB each Foundation that funds my organization as a customer:job.
3. Furthermore, I use the Unified Nonprofit Chart of Accounts that the California Assocation of Nonprofits provides http://www.canonprofits.org/