Hello Tracey,
You are free to set your policies as you see fit, and you can adjust your percentages at any time. We don't have any restrictions on how you decide to run your affiliate program beyond saying that you cannot charge affiliates to join your program. Everything else is up to you, you can pay affiliates on the schedule you like or decide not to make payments during certain periods, etc.
We do recommend that you communicate your policies clearly to your affiliates though, so that there is no confusion about when payments will be made or why a certain sale is coming up at 0% if you changed the rates.