The rent for the charter generally covers just the rental of the boat and crew, while all other costs (port charges, customs, utilities and other expenses) are paid separately. These additional costs are covered by APA, i.e. additional required costs.
The charter fee generally only covers the hire of the yacht and crew, while other expenses (all harbour, customs, utility and other additional costs for the vessel) are charged extra in addition to the charter fee. These additional expenses are covered by the Advance Provisioning Allowance - APA. The APA is usually 30% of the charter fee (sometimes 35% if the yacht burns a lot of fuel or if you intend to do more than 4 hours of cruising per day).
The APA covers the cost of fuel, communications, food, wines and liquors, dockage, etc. Any APA not used will be returned to you at the end of the charter as you leave. On the other hand, if expenses exceed the APA ( f.e., due to excessive cruising which can lead to high fuel costs, requests of rare liquors, etc.) you will be expected to reimburse the yacht as you leave the charter. This is rare but you need to be aware of this possible expense.