As a client you may choose where to go, what to eat and drink and so on. The APA is calculated to cover for most situations. However, if you plan to use the yacht for longer trips or if you have special requests for particularly expensive food and beverages it may happen that the APA does not cover all the expenses.
Your captain will keep track of your daily spend and let you know if the APA might become overspent. Overspending the Advanced Provisioning Allowance is perfectly possible. If this happens you may be offered to make another payment during the trip or before leaving the yacht.