Hi there. Generally speaking the easiest way to place the tug stops is to hitch the horse up and have them stand with the traces taut (perhaps on an uphill slope?) and position the tugs so they are vertical or slightly ahead of vertical as they would be when the horse is moving. Hold the tug stop up next to the shaft so the bump is behind the tug and up against it, then use a white pencil to make a mark on the shaft through each of the screw holes. Repeat this on the other side, then unhitch the horse and pre-drill holes in the shaft at the marks you made. You don't want to accidentally split the shaft trying to screw in the new tug stops or dull the brass screws. Make sure of course that the two sides are even before you drill!
As for whether to put them on the sides or below the shaft, that's sort of up to you. For most carriage driving applications you will find them on the side of the shaft because the manufacturers expect that you will probably be using open tugs and the shaft is free to float up from the bottom of the tug loop. If that happens and the tug stop is on the bottom it can float right through the shaft, doing you no good at all. OH! But most breed show harnesses have wrap straps that hold the shaft down so if you really want to put it on the bottom it would probably be safe enough. For versatility however it might be a good idea to go with the more standard side location. It would also be easier to make sure the wrap straps were around the bump in that case.
I suggest you "put" the horse to the cart as some horses need to be farther ahead in the shafts etc. This is how I have mine set, ans it is standard for any pony this mare's size. Any bigger and I would have to move the stops ahead.
And to get a perspective as how it all looks...
For instance, it is hard to tell, but the following picture is a pony rougly her size and same harness..in the same cart and I didn't move the stops