In HW 5+ advanced, with multi channel audio you can have each of the master mix bus outputs recorded, each master mix bus output is recorded as a separate wav file. You enable the recording on the master mix bus setup.
For example, if you send a mix of all your front channel outputs to a master mix bus you can have HW record that output and if you send your rear channels to a different master mix bus you can have Hw record that as well; you will have two separate wav files one with the front and one with the rear outputs. Normally I send both my front and rear outputs to the same master mix bus for recording (and get one wav file).
There are eight master mix buses which can be enabled for recording.
Iain