Unfortuately I do not think this is possible - certainly not on CCM 4.2 which is all I have access to currently.
For CAR to work the CDR Format Enterprise Parameter needs to be set to CDRs will be inserted into database.
Some third party tools - such as Stonevoice BillyBlues - need this paramenter set to CDRs will be kept in flat files.
If your third party billing product uses the flat file option then the only way of using CAR as well would be to change the service parameter during a period when no calls would be made to allow the flat files to be inserted into the CAR database and then change it back again. Not really a sensible option!
Please note that this information is based upon version 4.2 - if 5 is different let me know!