There is a standard use of classes for non-profits.  They are admin, program and fundraising.  Under program, you can have a sub-class for each program, and you can run a P&L by each program.

Use customer: job or customer: subcustomer (in QBO) for each funder: grant.   The customer would be the funder, and the job or subcustomer would be the grant.  

I'm new to Projects but as it has already been said, you can only link a project to one customer:sub-customer.  I think Projects is a good way to track income and expenses for fundraising/events.