If you use special payment conditions, then you obviously want to let that work without hassle in BookYou. See below for a clear explanation about this.
How can I explain to customers that I want 50% of the payment before the event, and 50% after the event?
You can enter the standard payment conditions at the module "PDF annexes".
End the content text of your confirmation or contract (you can choose one of these at the bottom of the page booking settings) with this sentence: "Unless stated otherwise at comments".
If you deviate from your usual payment conditions at a specific booking, then you can state that at the "comments" box in the contract. If the payment is partially paid, then you can state this at the internal notes of the booking.
It is important that you do not select a date at the field "date paid". You must do this when the full amount is paid. This way, an reminder will be sent to the client about the remaining amount. You can change the text of the payment reminders at the module "periodic e-mail" in the following text: We noticed that your payment hasn't been paid fully or partially.