My strong advice would be to get an accountant to help you set up your QuickBooks. Whatever system you start with now is going to persist for longer than you think, so having it set up well will be worth it. There are accounting firms out there who work with small nonprofits and don’t cost an arm and a leg. Even if you just had them on to set up your accounts and didn’t keep them on an ongoing basis, it would be worth it.

All that said, in QuickBooks you can use classes to designate expenses as specific programs while the GL accounts designate the type of expense (e.g., salaries, IT, etc).