When client/matter is established, there is an option to set the matter to Hourly or Fixed Fee. If a matter is deemed hourly, every time entry has the option to be set as non-billable or no charge. See image one below. This function has two purposes.  First, it allows you to track how much non-billable time is allocated to a specific client and/or matter.  Second, you can show that time as non-billable to the client on the invoice.  

The line item on the invoice will show the date and description but you $0.00 as the rate.   This is illustrated in the second image below.  This non-billable time can also be viewed in a timekeeper report.  

Image One:  Non-billable time function. 

Image Two:  Draft Invoice with non-billable time.
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Image Three:  Time Keeper Report