There are a a number of different ways you will be able to receipt the payment against a client invoice.
First you need to be sure of which account this will be receipted into, as payments using the Clients Trust funds use a different method than if receiving into one of the Business accounts.
The method used will also depend on system Roles and access - the book keeper will have full accounting access and for non-trust payments we would then recommend receipting via the Accounting invoice lists as the is much faster than opening each action in order to make payment. However, a legal assistant may only have access to do this via the Action.