Network DSCP traffic origination .... conceptual/practical help!

Question

Hello!
This is a very basic, but I think important inquiry... I am giving myself a crash course on VoIP/QoS and have some trouble with the foundation of it. Some is conceptual and some is practical.
So far I understand the ip precedence, DSCP and different types of shaping, etc. I found that on the call signaling side we were missing to detect under one policy the CS3 and CS6 traffic... all voice media is, apparently, marked EF and guaranteed bandwidth percent.
I don't have the luxury of a lab right now, and have been trying to optimize our voice on the locations with poor bandwidth (1.5Mbps T1) ...
One thing I don't understand is how this traffic is originally created with the marked header? Is it the actual cisco phone? is it a setting in call manager? is it call manager itself? is it because of the specific command or configuration within each switch "switchport voice vlan 100"? is it the combination of some or all of the above?
I am trying to learn as I go. I have foundation, good understanding of networks, traffic, packets, routing, etc. Some VoIP foudndation... but lack a solid QoS foundation to better serve our immediate needs.
Here is what I developed so far and found to be useful, although I am unsure of the "input" service policy. It seems to have helped, but honestly I'd like to know exactly why. And what I lack is the knowledge of how the packets are created by what... If anyone can shed some light here it would be a tremendous help!! Thank you for reading!
access-list 100 permit udp any any range 16384 32767
access-list 100 permit udp any any range 5060 5100
access-list 100 permit tcp any any range 5060 5100
access-list 100 permit tcp any any eq 1720
class-map match-any call_signaling
 match ip dscp af31
 match ip dscp cs3
 match ip dscp cs6
class-map match-any voice_media
 match ip dscp ef
class-map match-all inboundvoip
 match access-group 100
policy-map voip
 class voice_media
  priority percent 50
 class call_signaling
  bandwidth remaining percent 20
 class class-default
  fair-queue
policy-map mqc
 class inboundvoip
  set ip precedence 5
 class class-default
  set ip precedence 0

Answer 1

Thank you very much for the response!!
That makes sense... Now I just need to dip my head deep into Call Manager...
So if I take it from the top and track, trace and make sure all is marked properly... I could even config my switches to process/prioritize packets with ip precedence X and queue the rest...
Cool! ... Thanks again Sr!