To clarify, you will always get 100% of every sale straight to your own PayPal account (or through any other payment service you are using). If there was no affiliate involved in the order coming to you then that's naturally all yours to keep.
If an affiliate referred the order we'll let you know and tell you what percentage of that order they earned based on your settings so that you can pay them out later, but there will never be a cut automatically taken out of your sales due to our affiliate system.
Since we can't intercept or redirect any of your sales money it will be up to you to pay out your affiliates, which most merchants do via PayPal on a monthly basis. You can run reports from your E-junkie account to help with that, but you are also free to set your own schedule and means for payment as long as you and your affiliates agree to it.