Thanks for your feedback. Unfortunately, this option was never built into the original integration between the two systems. The integration itself was designed to be a simple transfer of data as it would appear in a basic journal for instance.
If you would like to alter these figures and have an individual nominal code for each employee you can do a manual journal entry or edit the entry once it is passed over?
If the request does receive plenty of votes and is a top requested feature we can certainly look at strengthening the integration further.