As mentioned in the garden shed some part are inter changeable. And when we do this shed we keep them that way until we do a full frame fit it.
Once a brace has been fit to the post or tie beam it is labeled for that location.
One method we have used is to make a unique symbol on the tenon and the same symbol on the mortise housing. So that star labeled tenon goes to star labeled mortise, for example. These unique symbols are made with pencil or magic marker as the time period from full frame fit up to raising is usually only a week or two at the most, so the sun won't have time to fade the markings.

You can mark the timbers with a chisel and label them as Raphael has mentioned. It is a good system, and you need to have it written down on your plan for future use at raising.
We designate one side of the building to be labeled with a 1 1/2" chisel and one side to be labeled with a 2" chisel. So bent one will have two posts labeled with the roman numeral I but they are different sizes.
We try to always label them on the layout face and at the top of the post, or some other standard location could be used.
Some other timber framers label braces at the post end, only. This make sure that the brace goes into the correct mortise.

You can develop you own system if you want....

Jim Rogers