QoS markings are applied by the handsets as well as the phone system, and honoured by the switches. Sometimes the switches will apply the markings if the customer doesn't trust the voice system to do it properly.
I'm guessing you might be referring to the fact that one VLAN (per switch or wiring closet) has the "voice" command issued to it. Although that provides some QoS configuration shortcuts, the main purpose of that is so that LLDP can advertise it to the phones, saving you from having the phones do a double bootup to get on the correct VLAN.
In any case, QoS within the internal LAN shouldn't be doing anything - it's on the the way to the WAN/internet that you hit bottlenecks. Mind you, there are some amazingly rubbish LANs out there....