There are different ways to charge for bookkeeping services. Most will charge by the hour, which if you are paid as a employee is the normal way to charge. This is fine as a employee, but very old fashioned for a freelancer.
Bookkeepers can be experienced, and many have also had formal training to improve their skills. For these reasons a freelance or self-employed bookkeeper should never charge by the hour. Instead charges should be done per transaction in varying formats. It is the fairest way, as a good bookkeeper can carry out more transactions than a poor bookkeeper.