Internal Costs

How do others keep track of costings of "internal" works.  Client is a garage & has set up recording of time spent/parts used in maintaining its own fleet in the same way as if work done for outside customer, with each fleet vehicle as Customer:Job -->  ie clock time & raise invoice.  Obviously this means that VAT needs to be excluded & also sales / "customer" balance needs to be netted out for accoutns prep.  There must be a better way, although this way the processes used by the guys in the workshop are normal so the time/parts will not be missed off.