I've put a recurring exception day and a number of unique exception days into a calendar for a number of employees. These days appear not to be accounted for in the gantt chart. The time duration is not extended on the gantt chart to account for the days which the employees are absent. Obviously there is some way of overlaying the employees personal calendar into the standard calendar but I cant figure it out.

Any suggestions?

Are you using Manually scheduled or autoscheduled task? When you assign resources initially, Project will calculate the amount of work based upon the task duration, the resource's max units and their calendar. If you assign a resource with non-working time (exceptions) in their calendar, Project will not schedule work for them on non-working days and calculate the lower value of work but will not extend the task duration.

Take a look at the Task Usage view to confirm when resources are working on tasks.