The garden shed is square ruled so in theory some of the timbers are interchangable. ie: the front left post is identicle to the back right post, etc. Once timbers have been test fit it's a good idea to keep the assemblies organised so they go together as tested.
There are any number of different ways (both traditional and new) of marking timbers, usually marks are made with the framing chisel or race knife so a variation on roman numerals works well.
I started my house with a partial frame that had been assembled and marked with a large felt tipped marker using the former owners own system. I never did find all the marks (the sun faded the marker) or figure out what they all meant.
I use a french system which numbers the posts, beams are marked at each end with the numbers of corresponding post giving you it's position in the frame. The front left post is marked I, the next is marked II and so on down the line. The second post back fron post I would be also marked I but with a "countermark" which is a small slash like tail added to the I, a third post back would have two countermarks etc.
This is bent number four being raised, I'll see if I can get a shot of the #4 countermark and add it to this thread. You'll note the the marking isn't true roman numerals as the #4 is notated IIII and #9 would be VIIII rather than IX. The reason being that IX (9) looks like XI (11) when viewed upside down. Some people use true roman numerals and underline them to indicate proper orientation.
Hope this helps.