CaseFox is flexible to accommodate different invoicing scenarios.  Suppose if you want to track time (and expenses) for your internal use but want to invoice your client a lump sum amount, you can create “non-billable” notes (simply uncheck “billable” checkbox on notes) for time tracking purpose and finally when you are ready to invoice your client, create one “billable” note (and in stead of entering time, enter the cost directly).  This way, the invoice will include only this one note.
Negative amounts may be entered in notes to show received payments or special discounts.  If there are some special fix value taxes/fees, those may also be entered into invoices via notes (just create a billable note for that amount and enter description).