I have both sets of pre-outs split just before they reach the amps, this minimises loss, but it does mean the head unit works a little harder for an equal amount of amplification. It is still preferable to running the amps from the speaker cable outputs from the headunit, as the unit is not having to supply power through these feeds. Its swings and roundabouts really - better quality, but a lower amplifier:headunit amplification factor. It wont effect the maximum volume your system will kick out though, this is determined by your amps at the end of the day.
