Let me start by stating I'm no pro at what I do. I just enjoy sharing how I do it. My methods may not be considered correct or they could be!? I'm just going to tell you how I do it.
First things first. When your working with natural stone from bulk or a pallet you need to gather all the largest stones and put them aside early on. If you don't you will be un-happy later. This image show all my cap stones I been stockpiling.
This wall is 20" high to the top. So what I'm doing is build to about 16" +/- . The reason for this is because with the natural stone caps I'm using they very from 2-6" in thickness. By building the wall to a point below my top string line this gives me the room I need to work backwards. What I mean by this is that you find the cap stone you plan on using. I'll set it on the wall then measure down from the string line or my top of wall mark. (a 8' level is being used in the photo) Next you must fill the void between the wall and the cap stone. Looking at this photo I can now measure the space then find the correct stones to get me to my height. Some times to keep it easy I'll just set the stones on top the cap to see if I now touch my string line.
I also keep a pile of small plates at hand. Some times plates can be hard to come by depending on the kind of stone your using. The plate stones I use to get my height. I always keep my plates close to my wall frames making them easy to find when I'm ready for them.
You can see different sizes of my caps stones in this photo. You can also see how I use small stones as I'm moving down the wall to get to the right height. As I call it working backwards. Your no longer building up the wall. Your now building backwards. You will also see a bit more then the 1 over 2 or 2 over 1 rule. You can see a 4 over 1 running joint. But little hard to void this sometimes. All rules are meant to be broken with the large cap next to a small cap. Do I have much of a choice. - Not really just need to run with it.
This photo I'm running two lines one to keep my wall level the next for my caps stones which run up hill. I'm building up to a place where I then find my cap. Then work backwards to find the right stones to fill the space under the caps.
In this photo I have placed three stones on the corner I want to use. Setting caps are like doing flat work you still need to make sure they match well next to one another.
As I'm moving down my wall I some times use a brick with string to my rebar. This wall has a level top. I'll place several cap stones to the string line then move my brick and keep on building.
Brick with string line wrapped around it. By moving the brick down the wall this will limit the chance of having a hi-spot in a stone which causes your line to be out of level.
Just look at those cap's now look below them to see what stones I used to work backwards.
Wall-la - flat cap stones.
Wall shown in photo current build 10/12 Roland Park, Baltimore Maryland. Stone used on this job. Western Maryland stone mixed with PA Blue stone. Color of stones brown, tan, red, cream and blue - mat colors.