Your bonus will be your upfront opportunity cost that the non-profit will place on locking the property in until the drilling commences. Once the drilling commences and there is valid, substantive hydrocarbons (oil, natural gas, naturally formed gasoline, condensate, salt water -- anything commercially sellable that is valid to mine for under aforementioned lease), then the royalties are paid to the non-profit.
The royalty will ultimately be what you receive on a periodic basis, and is based solely on the percentage in which the non-profit is due per the terms of the contract (lease), and the quantity that is mined from the well. This can fluctuate, as you can tell, because the percentage that is agreed to, let's say in this case, 20% or 18.75%, is a fixed amount. If it's oil, and they are producing 100 barrels a day for a year, but after that, the flow is reduced to 50 barrels a day, then the royalty will be reduced as a result of the flow dropping.
My apologies for rambling, but that's it in a nutshell. obviously Buddy has enlightened us to the percentage factor here as well. Hope that helps. The key here is the differentiation between bonus and royalty. If you have any questions, feel free to ask more. We're here to help.